Maybe I got the distro version wrong. That's the version inside Template.pm, but the dist version is 2.14. Still, I don't have a problem with multiple [% END %]s on the same line. Perhaps you can post a script which illustrates the problem.

You can specify Template directives such as PRE_CHOMP and POST_CHOMP in your ttree config file. The ttree man page explains it, or you can do ttree -h to see all of the options. You may not think you are creating a Template object, but you are; ttree is just doing it for you.