My actual Linux X5650 is xeon_linux01 and it shows 44KhS but only pulls 28K H2pS on average. Sure, that's a decent margin, but I'm running a very stripped down version of Xubuntu off a USB, so I would expect a somewhat higher actual rate. Windows is pretty bloated in that regard and it can only be a drag on performance. So on average, my Linux box is about 15% faster. That's certainly within the realm of reason.
Running Linux off a USB stick might actually be slowing you down. I did for a while and noticed odd delays, which turned out to be I/O delays reading and writing from/to the USB stick. In the end it fell over (although part of that may have been the age of the USB stick and heat causing contact issues on the connectors).
A spare hard drive or an SSD would almost certainly be better, or working out how some distros load themselves into a ramdisk before booting, so the USB stick is not required while it is running.
I pretty much do the same on my GPU mining rig, I tested using a HDD and there was no noticeable impact on that, so followed the conclusion that it would likely be the same on this. I've got a few extra HDD roaming around but I'm not seeing much difference in my debug log versus my windows box. So again, I'm guessing the difference is normal, plus when I am currently looking at the leader board, I'm (at this moment) 15th on the Linux box in H2pS and to be grabbing much higher would actually seem incorrect as I know Tiras knows what they're doing and is pulling about the same.