I just noticed that autoconf 2.54-1 writes configure files with DOS CR/LF line ends! what's up?! I check "unix" in "default text file type" setup option and I do not have any CRs in the configure.in files!
autoconf is a perl program. There were some releases of perl that had a few issues with incorrectly using DOS line endings even on binary mounts. Try upgrading perl to the most recent release (5.8.0-5 for "regular" cygwin; 5.8.1-something for "test" or "experimental" cygwin)
-- Chuck
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