cleanertm,
Thanks for trying that. I toyed with the idea of doing just that for several months but somehow couldn't summon up the energy to go through with it. Now I will definitely try it.
Regarding running NIOS IDE in Linux vs. Windows I can say from my own experience that running the IDE in Linux is much more pleasant. For whatever unknown reason it is a lot snappier in Linux and I'm not just talking about the overhead of launching all those cygwin shells during building. The editing itself is noticably faster on my Linux box. I have a reasonably fast Windows machine and I quickly get into the situation where the cursor stumbles every three or four characters I type.
One drawback is that certain Quartus designs will not load under the Linux version of the IDE. I don't have a licence for Linux Quartus so I run Quartus on Windows, NIOS IDE on Linux. For the most part it works but on some projects I always get system ID mismatch (or verify failed if I disable sysid checking).
Andrew