I prefer to understand what's going on.
Can it have anything to do with to transactions i've send from my old wallet (which was with Qt on windows 7) to my new wallet (which is on Linux Mint with Bitcoin Core) ?
On the same evening i started with sending 0.0002 BTC to my new wallet, to see if public keys were correct etc. This transactions has also more than 6000 confirmations. And this transaction is now shown as available balance !
You have quite a strange issue.
But this definetly did not happen because of a specific set-up (regarding sending-/recieving- wallet).
This is most certainly an issue with core. Since your transaction propagated correctly and already got confirmed it surely can't be because of your QT-client.
As LoyceV already mentioned the
rescan-command should solve this issue.