Quartus II is NOT stable itself

I use the commercial edition of 7.1, and I too experience the occasional temporary freeze. I don't often get crashes though, except with specific functionality. (For example, trying to disable specific HDL message numbers in the Settings menu crashes Quartus for me every time.)

I can second your comment about the multi-threading, too. One particularly crazy thing I've noticed is that if I have nios2-terminal running then I sometimes have to exit it in order to start a new compile in Quartus, or else the compile doesn't proceed. Ridiculous!