Everything's Brown

Sounds like a bacteria or algae bloom, if you suddenly stopped dosing vinegar you probably had a nitrate spike followed by an algae/bacteria bloom. Then when you started back up you had a bacteria bloom again from a sudden jump in carbon in the water coupled with all of the nitrates.
 
I'm not familiar with vinegar dosing like I am with vodka dosing, but I only dose 10ml/day of vodka in my 125/40sump. You're setup is dosing roughly 20ml/day. Might want to either manually dose or cut back the vinegar.

disclaimer: I'm terrible at math so my calculations might be off.

are your fish tipsy ;)
thats a lot of vodka
 
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Update..... I performed a 20% water change, pulled the GFO out of the reactor and replaced with carbon. Now the water is crystal clear and the brown stuff on the rock is beginning to subside. Cleaned the muddy stuff out of the skimmer body and its beginning to make normal skimmate. PH is at 8.1 and never saw a hint of nitrate through the whole ordeal. I think it was a diatom bloom, but still not sure why. Sigh of relief..........
 

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