In case anyone's interested I finally sorted this out. It would appear when the PC was reset without shutting odwn properly it locked some temporay files in a /temp subdirectory. Once they were deleted running Mwcleanup finally seemed to allow Quartus not to think that there were locked files in use and boots fine again.
It would appear that Quartus and SOPC run just fine on Mandriva 2007.
Now I just need to get SOPC to recognise the NIOS directory so I can build a NIOS core. Nothing's ever simple!
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/mad.gif