My code wasn't using weak references, so if that's the problem, it must have been strictly internal to perl libraries.

At this point, it looks like the problem is instigated by the C program failing to properly close the socket after a previous communication. Unfortunately, Can't seem to reproduce the problem now.

So I now have the full diagnostic output:

Assertion ((svtype)((sv)->sv_flags & 0xff)) != 0xff failed: file "sv.c
+", line 5400 at /usr/local/lib/perl5/5.10.1/mach/IO/Handle.pm line 48
+0.
[download]

This is indeed in sv_clear as some mentioned earlier.