Hmmmmm ...
it was just an idea as we had exactly the same messages after we moved from Q4.2 to Q5.0 with a project that was created with q4.1 (with nios1.1) and we were unable to use the flashprommer too but quartus prommer via JTAG and signaltap worked. even the ide debugger worked !
it was just the ide that had problems with our target using the flashprommer
back to q4.2 and everything was fine.
So we just created a new "mktarget..." board under q5.0 nios5.0 and those messages went away without a single change in our project except a recompile under q5.0 pointing to this new target board