Is the PCI bus really limited to 50MB/s though?
No, it's 133MB/s.
Agreed, the card isn't performing as well as it should and I'm not sure why. It's at times like this when I take a step back and think "is it worth spending x hours trying to fix this or do I take an evening to nuke the PC and start again with a setup that I know would fix the problem?"
Looking better, try the long bench in HDTach, it should give a smoother curve. Also check that the caching is enabled in the Intel Matrix Storage application thing.