Hey,
I was having the same problems with my bike before I went fixie. For my case, something at the rear sproket was making this ... kunk ... kunk ... noise 2.75 times per a single crank-turn or so. That was dead give away because my gear ratio was 2.7~2.8 I think. You ought to count the number of your noise and compare to your gear ratio ...
Anyways, I figured out the noise came from the sproket (freewheel) wabbling sideways. So somewhere in the latching positions, your freewheel goes out of alignment enough to hit against the chain plates causing the annoying recurring noise that just kills the SS (or fixie) patented quiet ride.
I searched every where and a lot of people have more success replacing their freewheel than lubing them. (Someone recommended dropping some Tenacious Oil.) Many people suggested going for White Industry stuff, but I just got fed up with it and went fixie.
T