DMA Transfer problem

After you have a minimal system, if you still see the problem I would simulate the software running on the CPU. You might see something in the simulation that will give you a clue as to what is happening.

Another thing you could try is using the macro file from the DMA driver and write the source, destination, and control fields directly to see if the behavior is any different. I forget what the file is called but it will probably be something like "altera_dma_regs.h".