Nicole, Which problem are you reffering to? Do you have a KnowledgeBase document ID? Also; I'm not sure I understand why debuging the exe would be a pain. Sorry I was not able to help more, please elaborate on your problem and I may be able to do something.
link to KB ID: http://digital.ni.com/softlib.nsf/954feaeea92d90918625674b00658b83/ab94b3a08673e33286256af100588e07?OpenDocument
It is a pain to debug the VB exe because I cannot use the normal debugging tools provided in the VB interface if I can only launch the executable to try it out. Imagine trying to debug a VI without the debugger.
The problem is that when I load Visual Basic and use it to call a DLL created by NI App Builder, I get an error "unable to initialize NIPALU.DLL". I am able to successfully run the VB executable from the command line.