Could be a bad Thunderbolt port, a failing Thunderbolt-to-FW adapter, a bad FW port on the TC, or a failing Impact Twin. Please create a System report and send it to us by email; it may give us more information on what's going wrong.
In general, for these types of individual setup connection issues, it is more efficient to contact us via email so we can gather additional information specific to your particular system that you probably don't want to share with the world at large ;)