Do the changes work when you edit /etc/proftpd.conf directly? This will tell you whether it's the lines in the file or the custom template stuff that's causing the problem.
You do understand how the template fragments work, right? Just figure out where in the file you want the new lines, find out which fragments in /etc/e-smith/templates/etc/proftpd.conf/ contain the lines near where you want your addition, and stick your new/modified fragments (with the proper name to reach the desired location in the file) into /etc/e-smith/templates-custom/etc/proftpd.conf/.
And a problem I ran into once: You're not creating the new fragments on a Windows system are you? The text files are formatted differently, and Linux won't be able to read the file as intended...