Hi CaptainAfro,
Let's see. Before you install Powerstrip, you need to check if all Soft-15khz modes work properly. The change I suggested only allowed GroovyMAME to pick from the various resolutions Soft-15khz had made available, exposing the failure of some of them. So my advice is, use ArcadeOSD or any other means to test each resolution individually. If many of them don't work, then definitely that's not a suitable card for GroovyMAME. GroovyMAME assumes that all the resolutions available are in working order, there's no way it can anticipate one of the not working.
Powerstrip would only get into scene after this, to allow specific tweaks to each resolution in order to reproduce the original refresh rates of the different games, which are not all covered by the defaut resolutions installed by Soft-15kHz.
Regarding the problems you're seeing switching from 800x600 to 640x480, bear in mind 800x600 is a rather extreme resolution for an arcade monitor, it can only be possible by lowering the refresh to 49-50 Hz, which is quite different from the usual 60 Hz. Besides, if you adjust v-size for 600i lines, you'll see huge black bars when you switch to 480i, this is how things are with CRT devices.