okay, it's fixed now, so I guess I'll just report on my findings.
First of all, I was using a uni-bios version 1.3, and an MV-4F consolized unit.
Anyway, when I was in USA Arcade mode, and even though I had the hardware setting set up so that it could switch freely, the unit wasn't switching freely between games via the select button.
I just happened to switch the unit to Euro Arcade mode, where the "SETTING UP THE CABINET" options are ever so slightly different (the 1P and 2P coins/credit ratios can be changed independently in Euro mode). Here, I noticed that the game was set to switch only when credited. After I changed this back to switch freely, everything worked fine in both modes. Apparently, the Euro setting takes precedence over the USA setting, regardless of which mode you're playing in.
Oh, and to get to the options that I'm talking about, you do this:
B+C+D (at bootup screen) --> SETTING THE SOFT DIP --> SETTING UP THE CABINET --> GAME SELECT, then change this so that's it's on "anytime" (when in Euro mode this is called "free", and this one DOES need to be changed).
On my machine, you must do this in Euro Arcade mode for it to take effect.
Just thought I'd write this down in case anyone else runs into the same problem. I found it to be a little unintuitive.