After playing around with things here and there over the past month, I'm fairly convinced that there maybe something strange happening with my monitor. It has a slight vertical shake that happens occasionally (more frequently before it warms up). Oscar has given me a few suggestions as to where the possible problem might be (cold solder joints on the pins to the cards), but I haven't had time to implement them. Another clue as to being the monitor is the fact that when I turn a gun into calibration mode, instead of seeing a completely white screen, the screen has some gradient ripples in it in the horizontal direction (more promiently on the left side of the screen). I have to post a picture of it sometime so you know what I mean. The ripples aren't there when playing games however. I don't know what is causing them.
I'm running my desktop and all the gun games at 640x480 with HWStretching on. This seems to have been the best thus far. The kids have never callibrated the gun after starting up, and it seems somewhat playable (but the guns have never been really accurate with my monitor, even with a somewhat good callibration). Also, I am running the USB VGA guns, not the TV guns. I was using Ultimarc's video amp with my ArcadeVGA card, but it was also causing some issues with the guns. I removed the amp and used an old VGA cable (slightly hacked) to hook the monitor, and that's working fine now.
If I can't fix my monitor, I'm not sure what I'll do. Replace it with another arcade monitor? or standard VGA monitor? As much as I like my arcade monitor, I've been leaning towards a standard VGA monitor for a couple of reasons. 1) It would probably work better with the USB lightguns as that's what they were designed for, and 2) newer monitors can turn themselves off to prevent burn-in and save energy. (I'm concerned about burn-in as our kids will often just leave a game "paused" for hours and the monitor never gets turned off, and due to some MAME issue, Windows XP will never start a screen saver when in this state)
Okay, enough of my ranting, but that's where I am today.