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Perhaps funny to post a solved problem, but here goes:

Maybe this is of use to someone who is really scratching his head, took me some time to debug:

When starting the Arduino software, sometimes it would wait for a long time, and then disappear or give an error message. Only sometimes ...

I then noticed that my cellular phone went "bleep" during the start up of the software. It seems that when you have a bluetooth device paired with your PC and there is a COM port attached, the Arduino software will try to make a connection with said device, in my case my telephone. If you don't ack the connection on the telephone, the software will time out and exit.

Switching the telephone off, ack-ing the request or putting the telephone out of Bluetooth's reach lets the software start with no problems...