Since you didn't have the problem before, maybe you were too focused on trying to ensure having a good time, since you spent a month apart.
Is this your first year of college? That first year is so extremely stressful for so many reasons...whether you can sense the stress or not.
I wouldn't read too much into the "emotional problem" thing either. The first time I heard that rationale was on an episode of Sex & the City. I'm not saying that it's not true, because it probably is NOT a medical problem, but if you read too much into it, you'll just cause more problems.
It's also very refreshing to see that you're going to separate colleges and trying to work things out that way. That can also be very stressful and that line of trust becomes very long and hard to see...and that sometimes has an effect on the love life.