I just tried V4.3.4.4 on 2 Lollipop devices, a Fire new generation and a Nexus 7 2012. In both cases the Use templates everywhere setting sticks. I tried using "back" until the app exited. I "forced closed" the app. I did a backup, reinstalled the app, and restored the backup. I tried checking the other boxes then re-checking the templates box. In all these cases the "Use templates everywhere" remained checked.
Why you are seeing what you see is a mystery. Do you have some kind of auto-backup system in place that might be restoring settings from the cloud?
I can't see what a debug log would tell me, but it is probably worth sending one just in case.
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