... 'DOS style line breaks'. Could this be the problem?
Actually, yes, playing some more with this (in particular with a csh compatible shell), I do in fact
obtain similar effects when the entire script has DOS/Windows style line endings...
(just fixing the problem on the shebang line is not sufficient).
Not sure how those \r got in the file... did you edit Configure prior
to running it initially? Anyhow, this should fix the problem (at
least with this very file...):
perl -i -pe 's/\r//g' ./Configure
(Well, if you already have any perl installed, that is... Otherwise, look for some tool like dos2unix, or similar)