Clicking noise coming from cog on fixed gear
Is it the same link every time? There could be a tight/sticky link in the chain from when it was installed. I'm not sure why that would have come up after removing/replacing the wheel, but it's worth checking. 


Mark or otherwise make note the problem link
Take the wheel off or push it in the dropout to put slack in the
chain
See if that link is difficult to bend
If it is difficult to bend, then set your thumbs on it, push it side-to-side, quite
    firmly but not with all your might, until it becomes less sticky