I've never seen anything like this.
The code may be corrupted although this is not certain by any means. You could try Rob Bovey's Code Cleaner http://www.appspro.com/utilities/Cleaner.asp
to try and sort it. Otherwise I'm out of ideas.
There are, of course, standard reasons why events may not fire off (written about Workbook_Open):
1) If you turn off events, then workbook_open won't fire.
application.enableevents = false
2) If you hold down the control or the shift key when you're opening a workbook, auto_open and workbook_open won't fire.
3) If you are opening a workbook via a macro and you used a shortcut key for that macro that included the shift key, then excel gets confused and will not fire the workbook_open or auto_open.
But it doesn't sound like any of these are the problem.