USB has always been more flaky for me than I think it should be. Condolences.
(I hope USB3 is better, but I'm not holding my breath.)
Does it always work Ok if you plug it in after the system has completely booted up?
Is anything plugged into the hub when you try to boot with it connected? If you've got disk drives attached to it while booting, in my experience, Winders won't like it. I've got USB and eSATA drives that I have to power up after the system has completely booted, otherwise it'll hang. (Win2k). If you don't have disk drives attached, anything attached to it may be loading the port too much for some reason. If nothing's plugged in, it may be that Winders is having P&P issues with it on booting.
If it reliably works fine after the PC has booted, I think you'll just have to remember to unplug it before rebooting it.
HTH a bit. Good luck.
Cheers,
Scott.