I spent a long time trying to build a system from scratch and found that if i deviated from the supplied tutorial template it would not run successfully.
I then discovered that there was a service pack for Quartus that I had not installed and also a service pack and critical patch for builder. Once I had done this i found the systems that i had built from scratch ran successfully. Chekc for the latest updates on the Altera web page.
This may not be your problem but worth a try. I was also told that it is important to keep the versions of Quartus and Builder "in step"
Good luck
Conners