It is an IMAP account. Search messages returns no results when I search for text located in the body of the email.

In regards to the first link all my accounts/folders were already set this way. I was mistaken earlier, Once I select body from the search bar in the top right it will correctly find text in the body of my emails. I see that "Run search on server" was mentioned at the bottom in the comments although I can't find this check box item in the settings.

but is the wrong template still being used? Is this solved or not?

I'll create new templates as mentioned and see if the problem persists.

I have recreated the templates and filters. My old templates did have the same message ID upon inspecting the header info. After creating new ones each from a new mail the IDs changed. At the moment it all seems to be working correctly.