Hello,
I am not sure why the registry information in your MSI file is not being transferred into the App-V package (SFT) file. I am familiar with the CustomAction table problem that you outlined, and I believe it should be fixed in our most recent release (AS 9.5). Could you tell me what version of AdminStudio you are using?
Is the registry problem just present with a single MSI or with all MSIs that you have tried?
Thanks,
Ajay