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By Nios do you mean the Altera Nios2 EDS or the Nios II soft-IP core?
Some time ago, a customer to whom we sold the source files of the project had some problems when recompiling them in QuartusII under Windows and the problem was with license retrieval for NiosII Core.
Reading your post, it seems that the problem is not Nios but the tools.
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It's the NIOS IDE 10.1(Nios II Software Build Tools for Eclipse).
This problem is critical for University lab, because we can not grant administrator(windows) to all under graduate students.