Ed,
4 things I would check right off the bat, what exact wire size and kind are you using? Should be 14 Gauge Stranded quality wire, use the Lionel Spade couplers, or make your own from high Grade Brass Spade slide on couplers, wire equal to the Lionel Stranded. Use Gold plated Banana Plugs at the Transformer and MTH style Terminal Blocks running your DCS Track Wire. Quality everything does make a big difference.
Did you wire your FasTrack in Blocks using the 10 -13 Track Join Discipline, if not I suggest you do it, especially with FT. Engineer the drops correctly.
Next make sure you have not limited the Max Voltage being delivered to your Engine/Track with your DCS HHRC. I find guys doing this by accident all the time with their DCS, Legacy will be unaffected.
If your lighted cars have Incon Lights change them to LED's, Town & Country Hobby has all the different kinds for our Trains.
Good luck
PCRR/Dave