|Not sure this will help, using Excel 2000, on XP.|
If I open the first instance of Excel I will have only one process running, now if I open a second workbook from within this first Excel workbook, I will still have only one process running. Regardless of how many workbooks I open from within the first instance, I get only one process.
The only way I can get another Excel process to run, is if I then go to the START > Programs > Microsoft Office > Excel and explicitly start another instance.
Having both 2003 & 2007 running at the same time, would probably cause two separate process to run.
Someplace along the line I would guess that a registry entry got flummoxed.
Try running a Detect & Repair, and see if that help.