Seems like the Woodbury episode is a little further along in time than where we left the prison. Dialogue with Rick and the others made it sound like it had been maybe 4-5 months since they left the farm, so Lori wasn't far enough along yet.
Probably some time will have passed when we see the prison again. I'm guessing we'll see that they've settled down, begun farming, and are relaxing a bit. (I think they're taking a lesson from the farm and skipping over all the slow-moving stuff this time.) That also means the two plots will be in sync again — and Lori will be just about at term if she isn't late.