Thanks Zador,
Unfortunately removing it didn't help, but you're right about the consistent location of the errors, the problems seem to start around:
Do these values seem correct to you? This is using the latest build of the https://github.com/igorpecovnik/libtree.
I've also now tried a third, different brand and slower (Class 4) μSD card - hdparm removed - and the problem still persists but again slightly different output: http://pastebin.com/8wKpnwXz
I'll keep trying, maybe the next step is going back, reverting some of the patches to see which one caused these problems.