what was the total rendertime on the system - I mean is 10-30 secs a very small percentage ?

Also, are the times in Win2k and Linux repeatable ?

I don't know if its using the hard disk much but the hard disk is not a uniform speed across the platter (I know you said swaps were off) - is your Linux partition in the slower area? Although to be honest I wouldn't have though this would have made a massive difference unless its thrashing the hard disk around a lot though - on some computations at work we can get hours of difference on a twenty hour moderately hard disk intensive analysis depending on how full the hard disk is and where its writing to.

Clutching at straws really....