I don't know if the incorrect selection of templates is related, but if this is an IMAP account, it seems that searching or filtering on Body text is still under development: http://gsfn.us/t/3249m

http://kb.mozillazine.org/Filters_(Thunderbird)#Filtering_the_message_body

Does searching, from Edit/Find/Search Messages, work properly?

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

Did you try the approach mentioned in the first link of my reply? As you can see, extra steps are required to search or filter messages on an IMAP server, e.g. "Run search on server" must be checked in the Search Messages window.

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?

Here is the reply I sent to the OP by private mail (while my account was mistakenly blacklisted):

I think the search that worked was with the Quick Filter Bar, which searches downloaded mail. The "Run search on server" setting is in the window that appears when you right-click an IMAP folder, Search Messages (this type of search is similar to the filter dialogue).

But even if you have everything set up properly to search or filter according to body text, I can't explain why each filter replies with the same template. Perhaps you are experiencing this bug: https://bugzilla.mozilla.org/show_bug.cgi?id=533229

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.