Somehow it seems that my debug.dll was flawed, I just couldn't get the debug modus to work in the described way. Good news is that I found the bug and it had nothing to do with the BonusCommerceModifier code. I had inplented the code into a mod of which I though that it was running okay. The mod gives the possibility to add resources to civics. This is an old modification from TheLopez
http://forums.civfanatics.com/showthread.php?t=172405&highlight=Civics+Resources . Shortly before implenting the BonusCommerceModifier I had added 3 "slaves" resources to slavery, but didn't gave that resource any function. Looks like the AI can't handle such resources well. After removing these resources everything runs with no problems again, but I still have to finish one game to be sure.
I have attached the current version of the BonusCommerceModifier, all changes in the code are marked with "BCM". I have changed the market, grocer and bank to have their gold output increase modified by some resources.