Charging empty battery with computer's usb is a chicken and egg problem.

N900 must be alive to negotiate with your computer for 500mA, but to be alive it must have power, and to have power it must negotiate with the computer...
I've heard it'll draw the maximum allowed (100mA) when "off", it would take a while before it has charged enough to startup (which uses more than the max 500mA even, let alone 100mA)... I suspect if you try start before that, it aborts and switches off as soon as it notices the battery is too empty.

Hopefully it works better with the real wallcharger that's able to both supply 1200mA, which should be sufficient for booting, and has a very simple method for signaling "it's okay to take as much power as you want".