As demonstrated in this quest, using Link->Item[] to recieve an item that normally increases a MCounter does not change the maximum.
http://www.mediafire.com/file/ndjakj3hhwz/BugTestA.qst
To reproduce:
One screen above the start is an empty chest, an odd tile out, and a small wallet. The empty chest gives Link the small wallet through Link->Item[] = true when he steps on it, and the tile gives Link rupees every frame with the cap set to the correct MCounter.
By default, standing on the tile caps rupees at 255.
If Link picks up the visible small wallet, the cap increases to 500, like it should.
If Link gets the small wallet by standing on the chest, the cap stays at 255, even though the subscreen shows he has the wallet. Only by picking up the visivle wallet will the cap be corrected to 500.
This bug appeared in at least Windows Build 1074, and exists in all versions up to current.