Hmm,
Looking at the screenshot, Tech To Level appears to be the culprit. I wouldn't rule out a possible bug with how CTEC reads/saves the stat. There's a couple of those unknown $9001's in the Magus data, which is strange. Try putting 1800 in that Tech To Level and see if that fixes it. Also, when modifying that stat, check to see if the Dark Bomb on Magus Tech screen number is updating with the same value.
BTW, very important, since all these stats are only loaded into memory on a New Game, it's very important you select a New Game each time, and not load through a save or save state. What I did was after Marle's first text line at the fair at night, in TF I put a Store 06 to 7E2980, and then a WarpTo 006. That puts Magus right in front of Gato, ready to check the stats or battle Gato for a level up.
With my in-progress patch I set the HP, MP, 7 main stats, level, Current and Needed Exp manually and everything appears to be fine.
Tonight I'll take an in-depth look to see if I can figure out what these 6 or so unknown stat bytes are doing. I'm now very curious to what they're for.
Chrono99, thanks for the screenshot. A question, would you happen to have a 2xMoinsCher.com account? There's a SNES adapter on there I'd like to get for my collection, but I don't think it's possible to buy from the site outside France (I'm in the US). I was hoping to find someone that could help with the transaction and I'd cover all the costs, plus a bonus for helping. The item only costs about 10 Euro + shipping.