I've been having serious issues with the template system since moving from 1.1 to 1.3. Not sure if it's related to this, but disappearing/missing templates were one of them.
Rebuilding master data usually fixes whatever problem I'm having, though it's rather annoying to have to do that each time.
In any case I figure it's down to something pretty specific since obviously it works fine for the majority of people. FWIW I did used to have TMS installed but I uninstalled it prior to upgrading as instructed, and the issues persist with all add-ons and APCu and OPCache disabled.
Whenever I have a compelling reason to renew my license I suppose I'll file a support ticket and see if someone who's more familiar with the intricacies of the template system can track it down. I figure it's something between the built in TMS, the way templates are compiled, and the deferred system.