+1 I just went through this the other day - I had forgotten to select something, and it didn't become part of the template. I just went back and added it and saved again, and all was fine.
I particularly love track templates for Battery 3 custom drum kits, where I have each cell routed to its own outputs - and have all of the audio tracks for each kit piece set up and routing assignments made, as well as levels - and multiple drum buses. I also have track templates set up for Kontakt 5 - with various multi-racks set up, (piano/bass/organ/strings, and other combinations as well), with the output section assignments made in Kontakt, as well as the audio and midi tracks defined in a track folder and such.
I just LOVE track templates, and project templates too, for that matter.
Anyways - I hope the suggestion for selecting all that you want included in the track template helps you get your issue resolved.
Bob Bone