From sparkeh.net

Just an update on my post "Making Installshield deployments silent"

After making a package using the above method I found that the machine was rebooting after installation even after attempting to suppress reboot.

Natually I thought that there must be something in setup.iss that was causing this and I was correct. If you need to stop a reboot in this situation, open up setup.iss, scroll to the bottom and change "BootOption=3" to "BootOption=0" and voila, no more reboot.