Flash Programmer in NIOS2 1.1

I had the same problem - and a solution...

There is a bug in the nios IDE in Version 1.1 which don't forward the fpga jtag-chain position to the flash programmer. So you have to do it per hand.

Adjust all settings in the flash-programmer window - press "Apply". Then the IDE generates a file called "xx_programmer.sh" (where xx is the name of the project). You can find this file in the xx/debug/ folder. Open it with a text editor - find the lines where the flash programmer gets called (these lines start with "$SOPC_KIT_NIOS2/bin/nios2-flash-programmer") and add " --device=n" at the end of these lines - replace "n" with the jtag-chain position of the fpga - with 2 in your case. Do this as often as the flash programmer is called in this file (two times in my case) then save the file.

Close and reopen the Flash-Programmer window in the nios IDE and press "Program Flash". DO NOT PRESS "APPLY" - or you have to do the modifications again.

guys from altera : please add this to your fix-list for the next update...