Why do I have to unplug the STM32F4 discovery card to update program?
Wreck a $5 passive hub instead of a $500 computer! 

Or find better upload tools...

If the newest release of the Atollic tools don't solve your problem, search "open source STM32 upload tool" - there may be an open source alternative, along the lines of "avrdude" for another family of CPUs.

You can still use the current tool chain for program development, as long as it can produce a standard executable format like ".elf" or Intel Hex, that the new uploader tool can recognize.