Turns out I'd disabled the error log and forgotten about it. With the error log on, it tells me:
[Wed Jan 30 09:17:26 2013] [error] [client 172.17.0.141] CGI ERROR: A system problem prevented your request from being completed.
[Wed Jan 30 09:17:26 2013] [error] [client 172.17.0.141] Premature end of script headers: kareha.pl
I tried opening kareha.pl in vi and changing the format to Unix, as I had been editing it to fix another problem (turning off strict subs) in an odd little iOS app, but no such luck.