Hickory: There's your problem right there. Trainers are hacks, and are never 100% reliable. You have undoubtedly corrupted your save file.
zerebrush: I do not think so: I used CHU on one save only. Continued to play with a save before the trainer test.
I understand this is VERY late to the conversation, but I felt the need to answer with a solution in case others have this problem.
Turn off the trainer's infinite potions/bombs function, use all your bombs and potions, then meditate. Your equipped bombs and potions will refill with a positive number. You can then turn the function back on. Keep in mind that you'll need to do this for every bomb listed as a negative number.
I hope this helps :)
