I keep getting the program compatibility assistant window pop up, saying
This Program might not have installed correctly
whenever I try to download my "setup.exe" file. If I cancel the window, the download continues and completes correctly. I am using clickonce to do this but that may not be relevant.

It didn't used to happen to start with. But I've downloaded the same file loads of times from various different locations now, and it's happening every time.
Can anyone suggest what is causing this?