Hello and welcome to our forums,
I cannot say why this happens, but we would like if possible to investigate this. Can you share with us your solution (SLN file) and all the projects it includes (only the project files without their source code)? If so, just send us your files by email to support at advancedinstaller dot com
Also, in the meantime as a workaround you can manually create from scratch your setup project. Have a look on our "Professional"
tutorial for a starting point.
All the best,