Yes, a bent BB axle is nasty on a fixed er, even single speed. But most often radial runout is caused by the chainring-crank assembly bolts. The bolts are not a tight fit, and while you put the chainring on the crank it can move a bit, while tightening the bolts, make sure the chainring is centered on the cranks.
Cpt Bike, Sheldon Brown, has an article about that, as you may know, he was an avid fixed gear rider.
http://www.sheldonbrown.com/singlespeed.html#tension
Same problem may come as I said from a bent BB axle but that is somewhat rare.