I believe the problem is in substituting several independent .exists targets with a single blibdirs target. Though I haven't investigated the exact details, you should be able to reproduce the problem with any CPAN module building dynamic extensions, I've just tested with DBI-1.39, every time I run make it runs:
Running Mkbootstrap for DBI ()
chmod 644 DBI.bs
rm -f blib/arch/auto/DBI/DBI.so
LD_RUN_PATH="" cc -shared -L/usr/local/lib DBI.o -o blib/arch/auto/DBI/DBI.so
chmod 755 blib/arch/auto/DBI/DBI.so
cp DBI.bs blib/arch/auto/DBI/DBI.bs
chmod 644 blib/arch/auto/DBI/DBI.bs
cp dbiprof blib/script/dbiprof
/home/stas/perl/5.8.3-ithread/bin/perl5.8.2 "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/dbiprof
cp dbiproxy blib/script/dbiproxy
/home/stas/perl/5.8.3-ithread/bin/perl5.8.2 "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/dbiproxy
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