Are you able to reproduce this on multiple machines?
If so, in order for us to further investigate this issue, can you please send us by email to support at advancedinstaller dot com the following resources:
1. the .AIP project file
2. a download link for your setup package
3. an installation log
If it is easier for you, you could create a sample project that reproduces this and forward it to us as well.
I suspect the issue was created because I selected "Keep Existing Permissions" and it was those permissions that were "incorrectly sorted". After sorting them it seems to have fixed it.