hi, the install.ptf file is typically located in:
c:\documents and settings\<username>\.sopc_builder
I've noticed a similar problem once or twice but it always seems to resolve itself after re-booting the PC. I believe that the problem occurred after installing the USB-blaster driver for the first time.
You'll probably have to contact Altera tech support about this because I'm reasonably certain that there isn't anything in the Stratix Development Kit that would affect the ability to find the install.ptf file.
If you have a reason to believe otherwise, please let me know.