Thanks for the vid! They came out spectacular!!!
As far aas the AEM 7, i have an older beta copy that worked for others. Heres the link. see if this one works. if not, ill try and recreate them and/or the installationand see what happens.
New Link soon to come
try deleting the old AEM7 SEPTA NJT files before installing. Just to make sure. The folders are here:
C:\Program Files\Steam\steamapps\common\railworks\Assets\RSC\NorthEastCorridor\RailVehicles\Electric\AEM7
in the AEM7 folder are two folders, one named SEPTA and one Named NJT, Delete these two folders ONLY then install the rwp from the link i just gave you. Dont worry, deleting the folders wont ruin anything. Ive personally done this many times. It will allow a clean installation of the repaints.
***UPDATE:So ive tried to recreate your problem. I deleted the two folders ive sugested and then installed the newer file for the Engines-NJT_SEPT_AEM7.rwp- and opened up the editor. Got them to show:

i really cant understand why its happening to you. Have you tried to just blindly place the engine on the tracks and see if the glitch goes away? It could just be when your placing the enginges. Its he only thing i can think of at the moment.
SECOND UPDATE: a fellow sim user pointed out a few issues with the files i packaged. Im fixing them now and will redistribute ALL of the dl files including the ones with just the engines. Posting the updates in a few.
NEW UPDATE: I havae reworked and repackaged the files. The new link is in the OP.