Good lord. I've been hunting down a strange SEGFAULT with the next release of extproc_perl, and after hours and hours of looking at perfectly good code, the culprit was...optimization flags! Turns out that ExtUtils::Embed is nice enough to let you specify your own optimizations, which in my case turned out to be nothing at all. I guess this makes sense since you're embedding Perl in YOUR program, and not building Perl itself. In any case, I decided to use Perl's optimization flags from the Config module, and voila! SEGFAULT gone.
And just for kicks, to further the definition of irony, at the time of the error I was implementing debugging functionality in my code! ARGH!