In your macro at the point you're opening the other workbook, inhibit
updating links and alerting the user for option inputs. I'd also recommend
opening it for read only, and inhibiting any macros that may try to run
anyhow. Try this and see if it helps:
Application.DisplayAlerts=False
Application.EnableEvents=False
'modify your workbook open code here
'open the workbook without updating links, and in Read Only Mode
Workbooks.Open "somefilename.xls", False, True
Application.EnableEvents=True
Application.DisplayAlerts=True
'now do your testing for VBA contents
'and end up by closing the workbook without saving changes
ActiveWorkbook.Close False