For starters, try and get a filename from the windows that pop up and do a reg search on that.
Win.ini: The run = line at the top should have nothing written after = If a file is written there (that is not obviously your printer or similar, backspace it till it only reads run = and save. Same with load =
System.ini Scroll to the line that says Shell Should read shell = explorer.exe Similarly, delete anything after explorer.exe
Now check your startmenu. I assume you have win98 or earlier if you have an autoexec.bat, so check in start/programs/startup for referances. Also check in the actual folder C:\windows\Startmenu\Programs\StartUp
If you get any filenames occuring in error messages, do a search for them and try to find a related program (eg an .exe file or .com file)
