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There aren't any such limitations that we're aware of. Script is hosted in VBP in much the same way that other hosts do (cscript/wscript.exe, etc.), and that has not changed between v5 and v6. We have never seen or had any other reports of script that just stops in the middle without any error condition, and both samples you provided display a messagebox as expected at the end of the build when built here. I would suggest adding more logging to narrow down at what line of code it is stopping for you.
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