stimmer,
Thanks, I will probably put the Bus Matrix stuff in. Maybe with conditionals so it's there if problems occur when I post this for test.
I was about to try the Bus Matrix next.
The SAM3X is new for me, I mostly work with STM32.
Configuring these things when your new feels like just try all possible combinations and something will work. Trouble is the number of combination for n choose m is mighty large. I tried both DMAC_CFG_FIFOCFG_ASAP_CFG and DMAC_GCFG_ARB_CFG_FIXED but not at the same time.
Edit: I have now run a lot of tests with 2 GB files using just the two DMAC changes. I have probably have written and read 20 GB of data without an error. It only takes a bit over eight minutes to read a 2 GB file.