I think, I nailed my problem: It is a Microsoft network thingy.
I am working with a Laptop that usually connects to a network. If I am not connected to the network, but have internet access Calibre seems to try to access external file systems and network printers. It then just waits for a few minutes until it gets frustrated or accept the fact that these resources are simply not available.
It seems to be an annoying Microsoft XP thing - so a simple vpn to my home network shortens the wait to a few seconds.
Thanks for all your input.
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