When reconnecting my laptop to an external monitor, the USB ports stop working
Thanks @Buscar웃 for answering this. The problem was Outlook. Dang Microsoft. 

Turning off Outlook before I reconnect the Thunderbolt display cable solves the non-responsive USB device issue. 



Huge bonus points to whoever can get MS to fix this issue in Outlook 2011. For those interested in the error messages associated with this issue, see the console messages link above.