12 feet between clip-on power supply is, in my opinion, way too far. You should have power supply every 6 feet or so.
You have to remember that power doesn't just flow up and down the tubular track freely. The metal track itself resists the power flow and restricts it. Long track sections like 12 feet can bleed the power down very significantly.
And, I have learned the hard way, that brand new track needs to be cleaned first. Manufacturing processes can leave films and residues.
Clean the tubular track thoroughly, and this can help alot. If you don't have anything handy, you can use 96% strength rubbing alcohol, and a good clean cloth with a tight weave, like an old undershirt, and run the wet cloth forcefully up and down the rails. This alcohol is flammable, so make sure you rub it off as you go with a dry cloth, and let it dry.
Using a weaker solution of alcohol, such as 65%, has too much water in it and can rust your tracks.
And, I'm not sure if you are running a separate set of wires to each clip-on or not. You can't just run one set to the first clip-on, and then run another set from the first clip-on to the second, and another from the second to the third. You need a separate set of power wires running to each clip-on.
If you do all of this, then you will probably have eliminated the track as an issue, and then you can move on to separately eliminate the engine and transformer.
Definitely start that process by cleaning and lubing the locomotive.
And, not trying to upset you, but you definitely have a bargain-basement transformer, and no transformer lasts forever.