Somehow I've got myself a "WTF" dilema with my newly setup Turntable. HELP!

Rhljazz
You refer to to a high output setting which is the exact opposite of what you want with a high output MC.  I looked up the spec for your phono stage and it provides a whopping 85 db on high and even a seriously high 60 db on the low setting.  Most phono stages provide 40 db low and 60 db high.

 I think you are overloading the input on the preamp.  Try the lowest gain setting.

WTF becomes TWF (That was fabulous) .  I do like a happy ending!

Great call, Rhljazz!

FWIW, in most situations in which an LOMC gain setting is inadvertently used with a high output cartridge, I would expect the symptom to be severe distortion on musical peaks, caused by clipping in either the phono stage or the input stage of the preamp or integrated amp. And I would expect it to occur on musical peaks regardless of whether one or both output channels of the phono stage are connected.

In this case, though, perhaps what was happening is that when both channels were connected to the amp the resulting overload was triggering one of its self-protection mechanisms. And perhaps the symptom followed the interchange of channel connections because the signal happened to be a bit louder at the particular time in one channel than in the other. Or perhaps a minor gain difference between the two channels was the reason.

For the benefit of others who may read this thread, one thing it makes clear is how important it can be, when seeking help on a problem, to state exactly what equipment is being used.

Enjoy! Regards,
-- Al

Thank you rhljazz, You were absolutely RIGHT! I set the dip switch as if
I were setting up a MM cartridge (low gain) and it works great. rhljazz,
you were cutting it a little bit short though, My wife is enroute to the
airport to pick up her inlaws, and the husband is interested in what a
decent current turntable sounds like. Now I can show him.
Thank you ALL for any input and suggestions you may of had.
And thanks to this forum, it has helped me in the pass, and probably I will
need some assistance in the future. MERRY CHRISTMAS to you all.

Typically, the choice of gain setting is made at the input side of a phono stage.  Many/most that provide both MM and MC levels of gain provide corresponding "MM" and "MC" pairs of inputs.  This makes sense, because in nearly all cases, the major portion of the gain is created at the first gain stage after the input, so that the RIAA correction can be effected with a higher level signal than would otherwise be the case.  This is only to say that I would be surprised if the OP's phono stage has more than one pair of output jacks per channel, and if selection among those choices has an effect on phono gain.  But only the OP can say.

Among the hypotheses offered, I think the "channels out of phase with each other" explanation makes a lot of sense.  In that scenario, each channel would work fine if the other channel is not connected or not producing signal.  No doubt we will soon know whether that explanation holds water, because it's so easy to test.  Even more trivial explanations could work: (1) Internally broken IC that is creating an intermittent problem; (2) "Iffy" contact between the hot pin of one IC and either the output jack of the phono stage or the input jack of the integrated; etc.

Try the phone IC into Left of Aux and Right of Tuner. See if switching sources still plays audibly.
Trying to ascertain if the pre/power amp is loading the phono amp incorrectly - i.e. a phone amp issue. If it does play on one channel for both sources and not when both are in one source input, I'd suspect the phono amp.

I propose you are confusing the setting for your cartridge.  You have a high output MC cartridge which will require the same gain setting as a MM cartridge.  So that means a low gain output setting.  

You refer to to a high output setting which is the exact opposite of what you want with a high output MC.  I looked up the spec for your phono stage and it provides a whopping 85 db on high and even a seriously high 60 db on the low setting.  Most phono stages provide 40 db low and 60 db high.

 I think you are overloading the input on the preamp.  Try the lowest gain setting.

Sounds like the preamp/phono stage as others have stated. 
First level of contingency is backup so,  
I would sub in your backup preamp/phonostage to confirm.
Good luck

Although some of the reported observations seem inconsistent with the possibility of a polarity reversal in one channel (which could conceivably result from a miswire in the new turntable, or even a miswire within the cartridge itself), to be certain that isn’t causing the problem I would suggest that you try reversing the + and - connections to one (and only one) speaker, at either the speaker end or the amp end of the cable (but not both).

As you may be aware, a polarity reversal on one channel can have strange effects on image position and focus when both channels are playing, but would not affect sonics significantly when only one channel is playing.

Regards,
-- Al

Tubes are my guess, on the integrated amp since all inputs give same results.  Is there a phono stage on your integrated amp you could try?  Gold Lion tubes are affordable.

It appears to be your phono stage based on your diagnostic results. You should swap the tubes and see if the problem follows the tube. If so replace the tubes. If not substitute another phono stage to confirm. If that fixes the problem send the phono stage for service.

According to my wife, WTF is World Taekwondo Federation. 

Thanks Al,
The phono stage (Jolida JD9II) was purchased new about 2 years
ago. I used it with another TT with rock solid performance, zero issues.
The TT (Clearaudio Concept) was purchased used recently. I just had
a new cartridge (Hana SH mc) installed and setup professionally.
Al, you are correct, all IC's are single ended. My integrated amp is a
Jolida Fusion 801. 

Strange problem indeed.

Is the phono stage new (to you), as well as the turntable? In other words, has this problem always been present since you started using the phono stage?

If so, although I can’t formulate a complete explanation at this point, my hunch is that something is miswired in the output circuit of one channel of the phono stage. Almost (but not exactly) as if a ground wire and a signal wire are interchanged, resulting in the signal on that output of the phono stage being shorted to the phono stage’s ground when a path between that signal and that ground is created by connection of the ground of the good channel of the phono stage to the amp’s ground. Or something like that :-)

Also, am I correct in assuming that these connections are via RCA cables, rather than XLRs?

Finally, can you indicate the make and model numbers of the phono stage and the integrated amp?

Regards,
-- Al

No balance control

Silly suggestion, but I assume that you've checked the balance control, if there is one ...

effischer, thanks for your help.

1)  Ground wire is secured. The gnd post is on the phono stage.
2)  Reversing IC's, music info moves on change.
3)  Replaced IC's, no change, same result.
4)  Changed input at amp end, All inputs render same result.
5)  Reversed tonearm IC's, No change of music info.
6)  Reversing the headshell wires (right to left and Left to right)
     did not change the location of music info.

Hopefully there is something here that triggers a possible solution.
Thanks again effischer 

I set up a lot of tables in my time, several times the problem was a ear pluged up with wax .

Time to run the isolation drill:  

First, Make sure your ground lead from the table (and arm, if applicable) is firmly secured to the ground terminal and that that ground terminal is secured to your mains (most phono sections do this internally).  This is likely not an issue for you because ground problems are very distinct, but check anyway since you'll be back there.

Second, switch the ICs right-to-left and see if the problem moves with the change.  

Next, change out the IC completely.  Any IC known to function properly will do for this test.

Fourth, run the output of your phono stage into "CD," "server," "tape" or "tuner" inputs.  It won't hurt anything but will tell you if your preamp has an issue with the "aux" input.

Next, reverse the tonearm leads into the phono stage.

Sixth, switch the cartridge leads r-2-l.  Be careful with this; you don't want to affect the alignment.

Last, if your cartridge is MM, make sure the stylus and cantilever assembly are fully seated in the cartridge body.

Those steps should at least get you started on identifying where the problem lies.  Good luck & happy listening!