Once you have downloaded the config into the memory of the keyboards, if the lights are still blinking, unplug the midi out from the computer. Something in your computer is sending MIDI signals whether you are playing or not.
This behaviour should stop if you unplug the MIDI out.
Modules and Hauptwerk only need MIDI in. So, unless you are configuring the keyboards, you probably do not need to have the MIDI out from your interface plugged into your keyboards.
If you unplug the computer interface's MIDI out and boot everything up again, you should be able to plug it in again with no problems.