Welcome to the boards..
here is how to fix the ropblem
Uninstall SFC 3 using Add/ Remove programs
Delete the SFC 3 game folder off of system
reinstall SFC 3, say no to Direct X 8.1 and say no to gamespy Arcade
Patch using SFC 3 Patch 1.01 Beta 2 Build v500, do not use the SFC Direct X fix, Do not use the Borg Bonus mission, Do not use the Nemisis Add On Pack...
all of that is included in the v500 beta patch and reinstalling it before or after the beta patch will cause game errors.. period.
after installing SFC and patching, use the SFC3 Setup.exe and set your screen res..
Make sure your Video card drivers are up to date.. NVidia just released a new driver this week
Run a Direct X diagnostic check.. check all tests (to run tests, click start, click run, type in "DXDIAG" click Ok)
if anything says out of date or anything but OK, reinstall Direct X 9.0b
find the shortcut to SFC 3, right click and select properties, click the compatibility tab, put a check mark in "Disable Visual Themes" then click OK
also make sure that your Windows XP Regional themes are set to the original language of XP.. AKA if your system is Win XP Language English but you set regions to Germany.. you will need to change region back to English...
After this you can add the Nerdlat bonus mission pack and / or add any mod that you wish to the game, so long as you follow the mod instructions of instillation.
Hope that this helps.