I have tried two installers - Setup2go, and Installmate Builder, and I have the same problem. At the last window of the install, I select the option to "Open program after installation finish", and sometimes (about 10% of the time?), my (Winforms) app's main window will open behind the Windows Explorer directory window I used to open the installation exe from.
The frustrating thing is - I am having trouble reproducing the problem reliably (the problem seems to occur around 10-20% of the time). I am using Windows 7 if that makes any difference. To clarify, if I open up the executable directly (rather than from the installation exe), the problem never occurs.
My knowledge on this kind of thing is limited - I recall a similar frustration happening with the MessageBox from this question
Any ideas?