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Unless I deactivate my second screen I have the regular mouse pointer on the second one, and when I click something in the game, the regular pointer clicks aswell and thus the game is minimized.

Is there any workaround other than maybe running it in windowed mode or deactivating the second screen?
This question / problem has been solved by dr.schliemannimage
As far as I know there are only three workaround for uour issue:
1) Disabling secondary screen.
2) Run in windowed mode.
3) Use a third party software.

There are some tools you can use to keep the screens indipendent to each other.
I think that and [url=http://www.actualtools.com/multiplemonitors/]Actual Multiple Monitors should suit your needs, but they are commercial products.
Dual Monitor Tools is open source, but I can't say if it could help you.