Trouble with Legacy set, any ideas?

May be track problem. Is the track on carpet or wood? Weight of engine may effect the track and if the center rail insulation is defective, that may be your problem.

Watch the following video. Are there other tracked above or parallel where the issue is?

I agree with Don.  While you can power through the section you are, likely, losing the Legacy signal due to a lose or dirty connection.  If you have some extra track, swap out the questionable section.  If not pull out the section and tighten and clean the connections.  It is also important that the Legacy base be plugged into a good, grounded, outlet so that you have a strong signal.

Plus, what Marty said.

Thanks everyone for replying on Christmas!  It ended up being a simple fix, swapping the extension cord.  Still doesn't make sense to me, but everything works perfect with the heavy duty extension cord!

The extension cord's ground wire (must be a three-prong cord) connects your base to the house wiring so the signal gets radiated by all the wiring around the train room.  If you don't have a good ground connection (I carry an inexpensive tester to verify the outlet), the signal is weak and inconsistent.

Blinking light means a signal is being lost.  I had this happen- turned out jumper wires added from the buss wire(s) to the outer and center rail in the section fixed it. 

@Tracker John posted:

The extension cord's ground wire (must be a three-prong cord) connects your base to the house wiring so the signal gets radiated by all the wiring around the train room.  If you don't have a good ground connection (I carry an inexpensive tester to verify the outlet), the signal is weak and inconsistent.

This makes sense!  Thanks.