I fix my own problem Get into the Darkorbit Client using Browser and put the PET Window on the Side of the Screen then go Log out and see if that worksQuote:
I'm having the same problem, the pet window is getting in the way of the 'mouse?' and my ship will just sit there trying to collect the box that happens to be behind the window.
P.S only started happening with the latest update 0.1.1.9
Solved.