NIOSII IDE 8.1 to 10.0 transfer problem

Having an 8.1 working project in CYCLONE III based on one NIOSII with some peripherals. The project includes EPCS controller, which is used for booting to an onchip Memory. Recompiled the project with Quartus 10.0 and IDE 10.0, no success, the CPU is not running. We are assuming the problem is with some new definitions in the BSP or something else. Verified the new 10.0 SOF file with old IDE(8.1) and it works.

Any ideas please.

Thanks