I have recently ran into a weird problem - having built a simple Nios II based system with a "selfmade" FT245R Avalon MM Slave, I am only able to run the code correctly with Nios II Software Build Tools for Eclipse. What I mean is, as long as I use "Run as" or "Debug as" and select "Nios II Hardware" all works perfectly - I can send data to the program via USB (and FT245R) and get replies. However, if I go to Quartus II (version 15.0) "Processing"->"Update Memory Initialization File", then re-synthesize and program my EP4CE10F17C8N chip (it's a CoreEP4CE10 board from Waveshare), the program runs up to the point where it's supposed to read from FT245R and hangs there.

Has anyone ever encountered such behavior? I wonder what I may have been doing wrong...