Taming a Bright Phono Section

Good cones like the Audiopoints might help a lot when used in combination with internal cabinet damping. You could be surprised! You could also be listening to electrical noise. Make sure your power is clean before drawing any conclusions.

The sound through the line stage is NOT bright. Plus I have set the
correct cartridge loading per Ortofon specs. I'm beginning to think
someone might have doctored the phono section. Or maybe it's time to upgrade the passive parts in the PS.

Did you get the very comprehensive instruction booklet that explains how to adjust for best sound? If you need it, I can search for mine, and make a copy for you.
Never bright in my experience, with Shure, and Grado MM cartridges.
Is there any trouble with brightness listening to CD's through the linestage?
I have two non-bright, proper sounding units in storage, as I could not bear to part with a "classic" design, when I converted to tubes. Another is still being used by a family member.
The suggestions above seem to cover most possibilities.

1. Cartridge loading, as others have mentioned.

2. Use the tone controls, as others have mentioned. (They are specificly made for the purpose of fixing your problem).Be sure that the knobs are installed correctly. You might have the treble boosted without knowing it.

I also used the Apt years ago and didn't find it bright. I used Supex 900 and 901 cartridges then. It is possible that it is simply more accurate than the Creek and your system is brighter than you like. You might try the Audio Technica OC 9 if you want to change cartridges.

Well, I had an Apt and I never found the phono section bright, but then I used a Shure VIII in those days. I think your problem may have more to do with cartridge matching - does your cartridge needs a load other than 47K? What does the manufacturer recommend? This could make a big difference. And, FWIW don't hesitate to use those tone controls on the Apt, they are well thought out and effective. They should help you cure the brightness you detect.

1. Try degaussing the phono section of the Apt Homan first using a cardas disk.
2. Clean the contacts with Craig pro-gold.

Now see if the phono section is still bright.