Thanks for the answers and suggestions! It feels like a wam bath after a frustrating evening
I have a processed number of blocks of 501568 (looks like thats up to date (?) )
But still there is a pending total of +/- 2.8 BTC
I can try to move the private key to Electrum (thanks for the suggestion!) But i rather do it as last resort.
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 ! (i would rather have it the other way around   first TX pending second available)

Final question: can i start rescan from the debug window? Or if that's impossible how do i start a rescan from a linux terminal?

Thanks for helping me out!

Peter