Here's another tip. To emulate what 2N2r5's little piece of tubing does, use a 3MM lock nut (plastic side up). I had a couple extras after replacing my stock jigsaw with the MK5. It works like a charm and is heavy enough and just the right size to not get knocked out of position. Haven't had a kink since, with ABS.

Doing a test print at the moment, 45 mins in and half way through it seems to be ok

This can happen if you take apart your hot end to try and clean it, or buy a self-assembly j-head.

If all the parts in the hot end are not screwed up enough so that they all touch, you will get a gap that will fill with melted filament and block.

The image below shows the filament removed from a j-head after I didn't assemble it correctly and it blocked. The wider filament on the left would have been in the PTFE sleeve. Then you see the largest diameter part of filament, this is where the gap between the PTFE sleeve and nozzle was and is the blockage.

The second image shows the same problem, but with the standard solidoodle hot end.

I've reassembled the J-head and so far so good with extruding filament only. About to a test print now...

If it happens during a print and I catch it soon enough, I can get away with pausing the print, doing the above, and then resuming.

For some reason the filament wouldn't go into the hot end but the head kept trying to force it in. The filament then kinked just above the hot end forcing out a loop that got bigger and bigger. I think the loop ended up sat just in the hot end.

is there filament trapped in the hotend already? that might be the cause...
if so... you might want to push that filament down further before you insert new filament... please give it a try.
I find it hard to push down existing filament with new string of filament... sometime i have to pull the existing filament out first before inserting. but in this case, it might be easier for you to push it down.. since i don't see anything for you to pull.

If you are still getting this issue after you realign it then you can try this.

What am I looking at exactly?

I am using standard print speeds.

I have since swapped the hot ends between my machine and the problem has followed the hot end so I have ordered myself a J-Head from eBay

Try adjusting it to be straight as possible. I recently had problems with my stock hot end and this. I think both of my peaks were shot from trying to print nylon waiting for my E3D to arrive leading to the comment below.

If this doesn't clear things up its possible your peek is melted inside and your filament is getting stuck inside. Or you have a slight clog in the nozzle.

What are your print speeds? Are you running extra fast or stock? If running faster try slowing down a bit. It's possible your heater can't keep up.

I'll try and get a pick later. If you are looking from the top down is your filament running through the gear into the barrel at a reasonably straight line?

Nope, it's off centre slightly...