The bug was weird actually..
if I had a simple system with just a DMA core tied to an SPI Device (I was trying to do DMA with my MMC core), and pipelining enabled, it would completely locku p the bus if I tried to even read an SPI Register without DMA enabled. I thought it was uClinux, so I used a simpel hello world in NIOS II IDE to read an SPI Register and it still locked up the system. I think they still have issues with pipelining, but only in more complex systems (I have 6 masters DMAing into DDR).
No rush for those patches, I'll send an upload point. Thx.