For reasons unknown to me, your setup has TM pick the Support folder included with TM rather than the one you svn checkout.
Aha! It turns out that my .bash_profile was setting both TM_SUPPORT_PATH and TM_PLUGIN_PATH for some reason. Those lines have been there a while, perhaps a very early version of TM or some plugin required that?
Anyway, I commented out those two lines and TM is now using the correct support folder and I can once again run perl scripts!
Thanks so much for helping to track this down,