Software Deployment

I think you need to open the project file, and find out what is the actual executable that it should point to.
The shortcut shown probably pointed to another backup copy of the installer file.

Note :The shortcut points to winscp406setupintl.exe Isn't that the original setup executable? No wonder it's launching a 'repair' - it sees that the product is already installed (by your package). Make the s/c point at the correct executable.

Having said that, if the setup stub is starting a repair, my guess is that it extracts and runs an MSI anyway and you have captured that to another MSI - never a good idea.

Start again. This time:
- clear your %TEMP% folder completely
- start the stub
- stop when you get to the first screen.
- Check your %TEMP% folder for an MSI. If there's one there, use that as your base and create a transform for any customisation you might need to apply.

Also, can I politely suggest using the correct forum for your posts? This one belongs in 'Package Development'. A moderator may move it at some point.