Could be your video card.. try this step and see if it works
fo into your SFC 3 game folder
Find the SFC3.exe file and right click on it, select properties.
in the grey properties box that pops up, click on the compatibility tab
make sure there is a check mark in "Disable Visual Themes" and click OK
if using an ATI Radeon vid card, set your desktop color settings to 16 bit color.
try game..
also, I suggest using the Public Beta patch v500 in order to get over 150 game bug fixes, the Borg mini Campaign with the fixed scripts, the Nemisis Add On pack..
however it would require you to reinstall as using the Direct X 9 fix with the Beta patch will corrupt the game as the Beta Patch already contains the Direct X 9 fix in it...
Hope that this helps.. if not, post back and we'll do another step.