Is it the shortcut creation in the program folder itself...or is it the shortcut creation on the desktop?
If it is the latter, don't let the installer create shortcut(s) on the desktop. Instead, copy the shortcut(s) from the program folder to the desktop. Mainly because the desktop has been "protected" by Microsoft in a similar fashion as the Windows root partition (for most people that would be C:\).
The first time an installer creates a shortcut there, you'll get a GUI message asking you to confirm if it is ok to do that. The installer might "squelch" this message, giving you the impression that it hangs, while it is just waiting for confirmation. Once the shortcut exists (on the desktop) you can alter it by script or GUI tool without any problem.
A fix could be simply running Process Explorer just before running the installer and 'pull' that window to the front. You could also ask the maintainer of the installer to either fix this or ask that he uses different installer creation software that can work around this behavior.
Personally, I hate shortcuts on my desktop, so I never create those to begin with.