Running skype 1.2.O.18_API, on Linux Ubuntu 5.10, on AMD64.

Skype runs fine, but if by chance I minimize the main window, it's gone and there is no way to get it back, unless i kill it and restart which isn't great...

Anyone have an idea how to fix that?

In your panels - Notification Area Panel is not present.
Add it, and Skype icon will be minimized there.