Why does my money keep disappearing. (Mom isn't collecting it either btw)

It just keeps going down. It was at 100,000, then suddenly 65,000 then I got it up to 80,000 and now it's suddenly back to 44,000

I'm not spending it on anything so where is it going :S

I Guess It's A Glitch Or Something

There could be several explanations:

1) If Mom stores your money, she may notify you that she used your savings to buy either a doll or an item. (Certain dolls can only be obtained this way.)
2) Whenever you lose a battle, you are warped back to the last Pokemon Center you used, and your non-banked money is halved.

It's most likely #2, as you said Mom isn't saving it up.
- DNA

Oh I see I didn't know that. Thanks DNA