Darius,
Sorry, I realized my error after rereading your post. Attached is an extract of the vmkernel log for the time period that the problem was happening. If you need me to expand the extract, I can do that, just didn't want to post the entire log file for you to have to wade through.
I also looked back at my notes from the original setup of the PCI passthrough. I had set it up because 4.1 wouldn't 'see' the SATA 6.0 adapter at all, so the only way to use it was to set up the PCI passthrough. 5.1 can use the adapter now, so I probably don't even need this. Fortunately, I hadn't put anything critical on the disks that were attached, I was only running some performance comparisons for 3.0 vs 6.0, and direct attached through PCI passthrough vs. virtual storage using VMFS volumes
Mark