You probably have a combination of problems here.
First and foremost, how often do you use acid to remove the Calcium Oxalate, aka "Beer Stone" or "Milk Stone"? This is absolutely required, and if you are not doing it now, your regimen should include an acid treatment every x number of cleanings or so, this is variable depending on lines, trunk size, previous maintenance, etc... but should be run every 3 to 7 times you clean the lines.
Additionally if the pieces are dark and brown like tobacco flakes floating in there, it sounds like the caustic solution that has been used in the past to clean these lines has not been strong enough, and soluble as well as the insoluble proteins have deposited with the Oxalate, and built back up over time. Strengthen your caustic.
Resting solutions in the lines is a good answer, and always good practic, rest and re-circ, rest and re-circ.
If you haven't run an acid / stone remover, that's likely your foremost problem, so start there and if not, let us know a little more about your regimen and hopefully we can make some suggestions.
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