Problems after using Safe Mode

I recently used Safe Mode to eliminate startup and shutdown problems I'd had with my Windows ME based computer. So far as I'm concerned, the problem is solved. But since then, after I've started my computer and entered windows, a box pops up with the heading "System Configuratioon Utility" stating, "You are using the selective setup for troubleshooting your system". Also, the blue error box occasionally pops up insisting my system is either busy or unstable. This had not occured without an actual error # until after I'd gone into Safe Mode. I assume there's something further I'm supposed to do in Safe Mode to rid myself of the first problem, possibly the second. Could someone Help me out here?