Atari 7800 Prosystem Issue

[Skyjay]

Hey all, 

So running through the regular setup process, i've ran into an issue with the Atari 7800 emulator ProSystem.  The system loads fine, but when it's in fullscreen more, the resolution displays in the setting I've chosen, but the colors are all wrong.  Almost like the color depth was set wrong way back in the day.  In windowed mode colors are fine, and if I go in and out of windowed mode to fullscreen mode sometimes the colors return to normal.  When the emulator is run on it's own, I get no color distortion going into and out of fullscreen mode.  Any ideas on what I should do next?  Thanks!