So just for if anybody looks back to this from a google search and for documenting it solved this issue (don't worry it didn't take 4 months!).
At the time I was using a precision piezo on the hotend using the printed mount. The bowden coupler that I had wasn't holding the tube firmly enough (even with a collet clip in there), so when I was retracting, the tube was being pulled up and away from the hotend. When enough extruding was done to push the tube back down is where a splurge would occur.
I figured this out by marking the bowden tube with some pen, and watching it move slightly further out with each retraction. I've now changed the mounting method (and z homing method too) and all is well!