As I said I am trying to use the Arena to level up my party. It seems I get normal XP for fighting the monsters but when I get to turn in the reward for winning a round (currently around 40) it seems that the points are substracted.

If anyone has a clue as to how this can be prevented I'd be happy to hear about it...

Yep, there is a custom patch by Jeff Ludwig.

http://www.jeffludwig.com/mm3/resources.php

I played a whole game with his mod. Works great. It even makes the game run significantly faster.


Quoted from his site:
This patch kit will remove the decryption of your MM3.exe file, and allow for the loading of a decrypted MM3.CC. A happy side effect of this conversion is that MM3 seems to run faster, as it does not have to decrypt data on the fly as it is loaded into memory. In addition, as of November 23rd, 2011, this patch provides two additional bugfixes:

Arena Experience bugfix— Arena awards its bonus properly (MM3 used to actually penalize experience if you had won more than 32 arena battles).
Damage resistance bugfix— This bug surfaces in the late-game when characters are hitting for tons of damage, and monsters have damage resistance. A 16-bit overflow occurs when multiplying out the resistance of the creature, resulting in far reduced damage. Damage is now calculated properly.