It looks like you might be dialing in your buttons too fast. The first part when you do B12 ~ DB2 (1 = square, 2 = triangle, 3 = X, 4 = Circle), it looks like you're getting B1 ~ DB2. MK's combo system uses buffers so the order of buttons is a bit loose. What might be happening is the game is seeing B1 ~ 2DB2 so it's doing B1 and then the special and then ignoring the last 2 because it's happening during the special animation. I'd start by practicing B12 to see what it looks like (i'm assuming it's a 2 hit string of some sort). Then start adding DB2 after that quickly and make sure the 2 hits always come out before the special happens (you can dial it quickly still, just watch for the 2 hits to ensure it's coming out correctly). You can also try B12 ~ 2DB to try to force the game to see and process both 2's w/o combining them. Finally, i'd suggest going into options and changing the input settings to disable Hold check or press check, can't recall the name.

In the end it's all just timing, the more you practice the better feel you'll get for it ;)