Sample Rate/Clocking. I see it at least once a semester. When you recorded, somehow you had an external clock set as the master running at 48k, but your session set at 44.1 (or vice versa). So, Pro Tools had a false idea of how fast it was sampling. Now that you are clocking to the internal clock of PT, running at Actual 44.1k, the song is playing back a touch slower, and thus 1/2 step lower than previously.
There's a few work arounds, but they're too long to type up at 1:30am. Quickest route is to plug in any external device digitally to your PT dig (adat/spdif) input, set it's clock to 48k, and set PT to clock off "external digital input". After you mix the song down, if you've recorded in Bwav format, you can find freeware to let you edit the header info in the finished wav file. Go in and tell change the header info from 44.1k sample rate to 48k, and it will play back at the proper speed.
A pain in the butt, I know, but that's the process.
Otw, pitch shift everything up with Audio Suite or Elastic Pitch, and speed it up with TCE tool or Elastic Audio. If the mix isn't *that* important, this is faster and easier.
