Do the DMA controller parameters in Qsys all function properly?

It depends on how you use alt_nticks. It's perfectly ok if you use it to count the bandwidth over a high number of ticks, but if you just use it to count how many bytes were sent between two ticks you'll get unreliable results.

Is the bandwidth increasing where you use larger blocks?

As for the incorrect bytes read back, does your Nios CPU have a data cache? If yes did you remember to invalidate the area you check, or to bypass the cache when reading the data back?