The PSU can throw up strange problems. And the one you describe with the 800x600 game screen not filling the monitor's screen is a strange one!
I play RB3D often here on Voodoo2 SLI. The game is about to be given a whole new lease of life by the Promised Land patch too around now (
http://www.wingwalkers.org/jasta1/newplmain.htm )!
I would suggest that since you have a workaround for the resolution issue you use it. Ideally changing the desktop res to run the game should be unnecessary. But Voodoo2s are getting old now and have to be humoured now and then. A utility like PowerStrip can be used to
automatically switch the resolution whenever you run the game.
The comet trails issue sound like passthrough cable interference. I run a desktop res of 1152x864x32@85Hz on a 19" monitor here and have no problems with passthrough degradation. But if I switch to 1280x1024 I start to see a slight fluffiness to text and lines. Do the comet trails disappear at lower screen resolutions?
There are a number of fixes for passthrough degradation. To quote from a Quantum3D support page -
1/ Lower the resolution and refresh rate.
2/ Try setting your 2D adapter to a higher horizontal frequency. In the Advanced Tab of the Display properties page, set the Refresh rate from "Optimal" or "Adapter Default" to a constant frequency of 75 or higher.
3/ Try straightening out the pass-through cable as much as physically possible. Straighten it out more by moving the graphics accelerator board into different PCI slot (See next bullet).
4/ Try swapping the graphics accelerator into a different PCI slot. Try all possible combinations. (Note: Windows 95 users may have to go through the "New Device Found" routine when swapping PCI graphics accelerators.).
5/ Use the manual video switching method #1: Leave the monitor cable unscrewed from the connector on the Obsidian2 graphics accelerator or the 2D adapter. Leave the pass-through cable that plugs into your 2D adapter unscrewed at the 2D adapter external port. When the Obsidian2 graphics accelerator is needed, plug the monitor cable into the Obsidian2 graphics accelerator and plug the pass-through cable into your 2D adapter. When the 2D adapter is needed, unplug the pass-through cable from your 2D adapter and plug the monitor directly into the 2D adapter, thus totally bypassing the Obsidian2 graphics accelerator.
6/ Use the manual video switching method #2: If DSUB inputs and BNC inputs are on the monitor, buy a BNC cable (If not already available.). Plug the BNC cable from the 2D adapter (DSUB end) to the BNC inputs on the monitor. Plug the DSUB cable from the Obsidian2 graphics accelerator video out to the DSUB input on the monitor (The supplied pass-through cable is not used in this method.). Use the monitor's video switching controls to switch between DSUB and BNC video inputs when appropriate (This can be extremely annoying if the monitor does not support automatic video switching/sensing between DSUB and BNC.).
7/ If two monitors are available then use one monitor ( #1 rated monitor.) and plug it directly into the 2D adapter. Use the other monitor ( #2 rated monitor.) And plug it directly into the Obsidian2 graphics accelerator video output (The supplied pass-through cable is not used in this method.).
Hope this is some help. RB3D looks fantastic on Voodoo2s. And the passthrough problem is surmountable although it appears to vary by monitor, primary card and quality of Voodoo2 and passthrough cable.
Good luck.