This is a tricky problem. It is the only problem I don't understand fully, as it has impacted about 10 customers so far, or roughly 0.5% of all Filastruder users. That makes it tough to collect data on and diagnose. I'll try to explain, distinguishing that which I know to be true from that which is speculation.
This part is factual:
Colorant/masterbatch is hard to come by in the small amounts we need - companies typically sell this stuff by the truckload. Often times distributors (such as OSP, etc) are able to pick up surplus masterbatch/colorant from companies that go out of business, etc.
This is mostly theoretical, just going on what little evidence I have:
It seems as though some companies sell master batch that is "universal" or "for ABS", but may not actually be universal or ABS. For instance, there are some "universal" colorants that won't melt at PLA temperatures. In about half of those cases, folks ran glow in the dark blue masterbatch just prior to experiencing the slowdown. My theory is that this masterbatch sticks to the walls of the barrel and reduces friction, which reduces the pressure the extruder can build.
The fix:
Some folks run straight ABS (no colorant) for a while and let it clear itself.
Some folks pull the nozzle and pull out as much polymer as possible with needle nose pliers with the hotend hot.
Some folks remove the hotend, heat to temperature, and pull the auger out.
Some folks soak the whole hotend in acetone for a week to soften the ABS and dissolve it.
Some folks have used a blowtorch to carbonize everything (i don't recommend this).
The last resort is replacing the barrel/auger. If you decide on that route, get in touch via the website contact form. In the future, it is probably best to stick to colorants that have been reviewed well. Some just aren't suitable for our uses.