Ok, so I figure I should start my own thread of issues here instead of just interjecting in other's potentially different problems.
I've been having very successful prints on my BukoBot V2 when there is little-to-no retraction involved.
However, when a job involves any sort of retraction, the printer seems to struggle to extrude enough once it returns from the travel move. I had limited success by changing my slic3r settings to extrude an additional 0.05mm after each retraction but it was just not consistent enough to eliminate the problem entirely.
It wasn't until last night however that I noticed something odd about the filament shortly after the problem begins. I stopped a job the moment I heard the extruder make a sort of skipping sound and then removed the filament and noticed this:
It seems that somewhere during the retraction process, the drive gear isn't catching into the same groove it previously created, which then leads to much thinner filament in the affected area. This would also explain why sometimes I will remove the filament only to find a semicircular groove ground out of it where the gear must've been spinning on the spot.
I've had the issue occur with 6 types of PLA, all from DiamondAge.