At peak MH/j Linux has a higher MH/s rate than Windows from the testing we did.  This probably has a lot to do with the fact Linux in general has a lot less 'overhead' than Windows.

I'll give you an example, card A is an ATI 5770 we found on this specific card the optimal MH/j was core 947mhz, memory 321mhz...  Under Windows this card averaged 197.9 MH/s over a 15 minute period, with those exact same settings we are getting 212.3 MH/s under Linux.  15 MH/s isn't a lot, but you factor in we were able to then remove the HD and the CPU load (and thus power usage) is lower, the Linux system has a much better profit margin than the Windows.

Now, our measurements aren't exact...  we took a network power switch/battery backup, and pulled snmp power usage every 15 seconds for a 15 minute period.  Then we wrote a script that would move the core and memory settings up and down until it found a sweet spot in MH/j for a specific card.  We ran this test on 8 different cards from 2 different vendors in the 5770 line, the results are similar for all the cards in that test.  We ran the same test on a smaller batch of 5850's and 6950's again with similar results.

If all you know is Windows, and you're setting up a single mining rig, then it probably doesn't make sense to worry about those numbers as much...  if you're trying to setup a bunch of rigs and plan to operate long term in a 20-30% profit margin...  every little bit of cost savings helps.

Not to mention, that writing a script to remotely move the core and memory mhz settings remotely in windows would not have been an easy undertaking.  IMHO (and it's just an opinion) Linux wins hands down as the better dedicated mining rig OS.