Alright I just figured out part of it. I reloaded my save in town, the one before I accepted the quest, and took a screenshot of my character sheet, clearly showing me at lv6. I then accepted a mission from the DB, after being promoted, and upon arrival at the dungeon, I have about six or seven skill increases. I then checked my character sheet and I am at level five! What in the world is going on? I've never had this problem before, and none of my main skills are decreasing. I am about to get a video of this phenomenon, but until then, I have screenshots for you.
http://dhta.oesm.org/sephiroth/fall_020.png
http://dhta.oesm.org/sephiroth/fall_021.png
*EDIT*
Here's the video, although it may take a day or two to become public. This starts at the load game screen and goes through me getting a quest and arriving at the location of my target. Could this bug be caused because I have a sword that improves longblade skill?
http://video.google.com/videoplay?docid=2171213273052929142&hl=en
Actually, the video is already up!