I've been working quite a bit with a C library recently. The original version of this library uses automake (i.e. the "./configure" stuff you see on all unix tools these days). Automake is the equivalent of ExtUtils;:MakeMaker for C tools.
Unfortunately automake is a big blob of scripting tools thrown together with a mix of shell scripts, m4 macros, perl code, and makefiles. It's really hard to debug.
The problem I'm facing now is that the library fails to work on Mac OS X. The reason appears to be that the .la file (that tells the library loader which files to look for - usually .so files) points to libfoo.so, but no .so file gets created. Add to that the library extension on OS X is .dylib (which also doesn't get created) and I'm in a world of pain.
Luckily there's someone at work who knows how all this stuff hangs together. But without him I'd be utterly lost.