I am 99 percent sure your problem is the blackening used on the center rail. I have used Alas track on numerous large layouts and always had to remove the blackening for trains to run well. Atlas is a wonderful track system but what ever they use to blacken the enter rail actually acts as an insulater and it also comes off on and accumulates on the center pickup roller. Unless you got some of the very early production with the flimsy joiners, their joiners that have dimples on the side work just fine. I used a fine SandFlex hand block by Kingspor which work great removing the blackening.
It is possible that a strong chemical like lacquer thinner might clean the blackening enough for rollers to make a good electrical connection but I could not make it work for me.
If you prefer not to jump and remove the blackening, take a multimeter and touching the leads to the outer rain and the center rail. Usually you will find you need to move the lead on the center rail back and forth or press harder to have it make contact.
Also, I never had any issues with TMCC or DCS by not connecting the two outside rails together. Remember, once a train car is in the loop, the wheels jump the power for one outside rail to the other anyway.
Happy railroading,
Don
