Electric contact

do you live in an area that has frequent lighting? 

did you leave your engines on the tract and the power supply and the tmcc system plugged in while you were gone?

Is the command base plugged into the wall or a power strip?  If it is a power strip, make sure it wasn't damaged from the storms.  If the command base had been damaged it should have affected all of your trains.  If it is only some engines make sure you still have a good connection to earth ground (third prong on the plug).

I don't think it's time for the repair shop just yet, best to do some preliminary diagnostics first.  I would think lightning damage would immobilize them totally, your symptoms seem to suggest poor connections somewhere.