Speaker phase observation and question?

" I have made a couple of observations. When connected in positive phase (red - red, black - black), the speakers put out pretty substantial bass, but the mids and treble are somewhat subdued. Upon reversing the phase, the mids and treble open up substantially, and the bass becomes somewhat subdued. To my ears, I actually prefer the reversed phased."

Somethings wrong. Even though your speakers don't use first order xovers, you shouldn't have that much change. Can you list your amp and speaker cables? Be very specific with your speaker cables. (brand, model, single or biwire,)

" Vandersteen also uses first order filters which don't honk up phase "

I have 3 pairs. I also had the exact same pair of speakers as the OP, and was able to do a direct comparison. Yes, Vandersteen is a better design, but I don't think that's the problem. If you look at the OP's description of the of complaint, it looks like a problem that needs to be fixed.

" When connected in positive phase (red - red, black - black), the speakers put out pretty substantial bass, but the mids and treble are somewhat subdued. Upon reversing the phase, the mids and treble open up substantially, and the bass becomes somewhat subdued."

I've seen several times where speaker cables were not labeled correctly. If the cables are terminated as a biwire config, and a mistake was made on either the high or low cables, but not both, it sounds like the OP's problem. One way the bass is correct, but the highs are not. After the swap, the highs are good, but the bass is now bad. The problem keeps going back and forth, and if you're not aware of what's going on, It'll drive you crazy.

Keep in mind that this is a guess on my part because we have no idea of what the OP's system is.

" I think if I could leave the bass in positive polarity, and reverse the polarity of mid/treble, the sound would be perfect. "

I'm not sure I understand what you're doing to change polarity. If you have high order xovers in your speakers, its true that the drivers will start and stop at different times. But keep in mind the designer knows this and factors it into the overall design. Its not something you would ever want to fool with. If you want to change polarity on the entire signal, you probably have a button for this on your Sim. Its a common feature on preamps and dacs. Just to be clear, I'm not saying that what you are doing is wrong, I just can't figure it out.

" Audio Art single shotgun run cables, with custom jumpers that mirror the cables."

I'm not sure what you mean here. Anytime someone says shotgun speaker cables, it means you are running 2 separate pairs of cable from the amp to the speakers. (For ease of connection, you can have the amp ends of the speaker cables terminated to one set of connectors. Its still a shotgun design). So, if this is what you have, the jumpers are not needed. It actually negates most of the positives gained from the double biwire.