open workbook using workbook

Hi All,
Just wondering how the best way to get around this problem?
I am using a workbook to start the main program. I am doing this as it checks to see if there are any updates to be done on the main program(also an excel workbook).
Once the startup workbook has finished what it needs to do I then open the main program which is all dialog box driven.
During its startup proceedure I then close the startup workbook, but because it still has a macro running, the main program also stops at this point.
I think I need to somehow stop the macro in the startup workbook completly before I try to close it. But I am not sure just how to do this.
I am using the 'Workbook_Open' event in both cases.

Any ideas? or is my logic wrong?

Regds
Phil S