To build Perl 5.6.1 from source, you must patch hints/darwin.sh to add the following line *OR* edit config.sh to alter the line:
OLD: firstmakefile='makefile'
NEW: firstmakefile='fmakefile'
The reason is the default perl distribution has this filename, a temp file, set to 'makefile'. Due to the case insensitivity of HFS+, the important file "Makefile" is deleted when the build scripts try to delete the temp file "makefile".
Note: I still don't have Perl building properly but this is a big step in the right direction.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20020203173059994