Hi iskh,
One of our engineers tried repeating your experiment here at Altera using a Windows ramdisk, ie, you convince Windows to use some of excess RAM as though it were a hard drive. However, he didn't find any difference in speed.
Do you know if there's anything unusual about your system (eg high disk fragmentation, running out of real memory) that might have caused an impact? Also, are the times you quote just for Quartus or do they include SOPC as well?
If everything appears to be normal, we'd be interested in having a look at your project to see if there's something funny going on.
Thanks,
Adrian Ludwin
Altera Corp.