And thanks for trying all that out! Well at least the game seems to know where your mouse is supposed to be in the world. Really bizarre...
One thing that the game doesn't mention, that I just thought I'd throw out there... is that if you are moving around (WASD) that'll cancel out any mouse input. So that you can't punch tiles and walk around at the same time.
But if you're standing still, THEN click on the cargo containers... they should get collected with a little progress bar. (takes about 1 sec)
I'm def going to keep thinking about it more this evening after work... see if I can find ways of reproducing it.