If I read you correctly, you set address book reply templates for certain contacts and when you reply to them the reply template in your address book doesn't get used.

The most likely reason for this is that you've got multiple address book entries for the same contacts, some entries with a template and some without.

So check for multiple entries for the same address (also when that address is a secondary address). Note that you can overlook entries when they're in a group while that group has the property 'hide when not explicitely selected' set.