Don't you just love it? Something is making a noise and you finally track it down. Sometimes it's two or three things that produce the same noise, rub etc. You correct one, it goes away but the other things get worse and it comes back.
What's more is sometimes you can't know what's causing it until each one fails successively, it's a learning process that sets you up to know next time and check each bit.
So... Lets start pooling that collective knowledge. Detail little niggles and problems you have solved that weren't obvious in the first place. It may be obvious to some, but it won't be to everyone and we'll have a great resource to check!
I'll start. My fixed wheel has been making a clicking noise for a while. Just a single click per pedal rotation. At first it seemed like poor rear wheel alignment due to basically rubbish hubs. When I got some new wheels that were well spaced it solved it at first. Then it came back and it seemed like the wheel was slipping. A quick loosen of the axle bolts and tighten would stop it for a couple of weeks. That was until last week when nothing would stop it, still just a single click, not hugely worrying but annoying. I considered whether the cog, chain and ring might be worn due to the previous problems but they all were fine on inspection. I took it out for a ride and noticed something funny, whenever I got out of the saddle it would stop clicking. Anyone guess what it was yet?
No! It wasn't the saddle
It was the bottom bracket. The non-drive side bearing had slightly collapsed, allowing the spindle to move in the channel. It was also the cause of the wheel alignment issues due to uneven tension on the chain when the bolts were tightened. This changing tension was causing the wheel to slip slightly over long periods.
I swapped out BB and the perfect silence of a fixed wheel drive chain returned
TL:DR annoying click thought to be wheel/gear related was actually non-drive side BB bearing.