MODULAR SGDMA burst read issue

This sounds like a bug I fixed a while back, make sure you are using the updated version from here: http://www.altera.com/support/examples/nios2/exm-modular-scatter-gather-dma.html

If the one you are using has a 9.0 directory in the zip file then you have the old one that had a burst truncation issue in both masters. Make sure you pass a start addresses that are compatible with the word alignment settings you are using. For example don't select aligned addressing then pass in some location that starts on a byte boundary for example.

Hacking the burst count is not recommended as there is a lot of logic dependent on the burst count (like the address incrementing logic).

If it is still failing I recommend capturing a transfer with all the read master internal signals captured.