It could be flash rust from the cleaning process. When using water to clean, particularly hot water, the barrel may start to form rust before you even get a chance to wipe everything dry.
I now use just cold water to clean my barrel, which seems to work just fine, and I don't seem to get flash rusting (at least to the point it is visible). After the last flushing, I run a dry patch down the barrel to swab out any moisture, then spray in some WD-40... run another patch down and then run a patch soaked good with Break-Free. I haven't had any problems with flash rust since then. I always run a couple alcohol soaked patches through the barrel before shooting, which takes out all the Break-Free. I have also tried a Hoppes #9 soaked patch in place of the WD-40 a few times, and that seems to work OK also.
If its just light rust, and not pitting, try your cleaning process over again... making sure to use cold water. Experiment.