I purchased a hobbed bolt of eBay (seller reprapping) and found just head of the bolt is 13.8mm accross. The gear is printed for a 12.8mm head, what I believe is the standard size. 12.8 mm also matchs the M8 nuts I got from the bolt shop. Has anyone else had this trouble ? I think another bolt is my best option at this stage.

hmm, strange. I had the same sort of problem, but that was a standard bolt and undersized printed part. in a pinch you could always heat up the end of the bolt and push it into the hole to widen it, but that's not ideal. You could always file/grind off the edges of the bolt a bit, at least that way if you mess it up you haven't ruined anything useful.

I've seen this sort of issue before with all sorts of bolts.

Cheap bolts don't seem to adhere to the standards, and M8 AFAIK specifies that the nut/bolt should suit a 13mm spanner (ie: ~12.8mm). I've also had the same sort of thing with washers being different diameters on the outside, which when they're on a rotating shaft can be a real pain.

Can you turn the bolt around and pad it with washers (to line up the hobbing), so that the threaded end goes to your gear? This leaves the head (with padding washers) sticking out of the end you would normally put the nuts on.

I have a Hyena, so effectively in my case it's the same both ways (both ends are threaded). I use a pair of nuts to "lock" the nuts on the thread, otherwise eventually it'll loosen during use. It's also the end I undo most, as I can hold the gear and then put the spanner on the nut to tighten/loosen - which beats needing to carry around two spanners when I take the printer somewhere.