NiosII trouble

I am having trouble with compiling a core and having it work fine, then re-compiling the core with NO changes and having the core fail to run programs. It will fail on download to SRAM or it will hang and never run the program.

I created a first geration NIOS V3.10 and it seems to work fine.

I am using NIOS II 6.0, Quartus II 6.0, SOPC Builder 6.0, NIOS IDE 6.0.

Custom board uses CycloneII EP2C20Q240C8 and IDT71V416 RAM. It is running a 40MHZ.

Thank-you in advance for you help!