Most games don't work properly in CGA because they manipulate the registers directly. Those that do probably did overly concern themselves with the refresh rate, probably because an IBM PC struggled to get 60Hz at all when lots of pixels were being manipulated.
However, none of the CGA registers have to do with the refresh, which is fixed at 60Hz and can't be changed.
Many games do manipulate the registers directly (all the Atarisoft ones except Pac-Man and Centipede for example), although in most cases it's just to set the palette. There are a few that are totally unplayable on VGA, like Jungle Hunt, which is so incompatible that DOSbox won't even run it.
Alley Cat does nothing of that sort because it was intended to be playable on a PCjr (like all the IBM gray box games), although it doesn't explicitly support it. Thus, it had to go by the rules and use the BIOS to set palettes and things like that.
What Quantum was referring to is the fact that it's choppy and difficult to play on VGA, which I've noticed as well. He also mentioned in his original thread some games like LSL and 3-Demon that don't perform well, either. I haven't tried any Sierra AGI games on my 5150 yet, but I did try 3-Demon and didn't notice that much of a difference. Snack Attack II, Wheel of Fortune, and Agent USA definitely run better on real CGA. The last one is particularly interesting because I tried it on my Thinkpad Pentium laptop (as it turns out, this 1984 game isn't timing dependent), and the animation was as smooth as on real CGA, but I assume that's because the laptop's LCD screen has a lower refresh rate than CRTs.
Interestingly, some games have the opposite problem. Shamus, Hard Hat Mack, and Frogger actually run faster on VGA.
