I would still very much like to know your MakeMaker version (output from perl -MExtUtils::MakeMaker=999) and some details about your perl configuration. Can you give the output from perl -V:'(site|config_args|prefix).*'? For example:

$ perl -V:'(site|config_args|prefix).*'
prefix='/usr'
config_args='-de -Dmksymlinks -Dusemultiplicity -Duse64bitint -Doptimi
+ze=-O3 -Dman3ext=3pm'
prefixexp='/usr'
sitearch='/usr/lib/perl5/site_perl/5.8.0/cygwin-multi-64int'
sitearchexp='/usr/lib/perl5/site_perl/5.8.0/cygwin-multi-64int'
sitebin='/usr/bin'
sitebinexp='/usr/bin'
sitelib='/usr/lib/perl5/site_perl/5.8.0'
sitelib_stem='/usr/lib/perl5/site_perl'
sitelibexp='/usr/lib/perl5/site_perl/5.8.0'
siteman1='/usr/share/man/man1'
siteman3='/usr/share/man/man3'
siteprefix='/usr'
siteprefixexp='/usr'
[download]

What I understand you to have reported (MakeMaker putting a module into somewhere not in @INC), shouldn't be happening. I'd like to find out what's up. (You might consider updating MakeMaker; I hesitate to recommend that not knowing how you have things set up--for all I know it might be having gotten a newer MakeMaker that broke things for you.)