Trouble building project with Cygwin

Some observations - not that they probably affect your problem!

Those scripts probably shouldn't be assuming that $0 contains the absolute path of the script. If a unix kernel processes the# ! it has to set $0 to something the process can open to get the script (which is why it is usually the full path), but the actual contents aren't well defined - it can be /dev/fd/n.

The $@ should be "$@" in both scripts - otherwise the parameters are subject to field splitting (bad news if there are any embedded spaces).

Might be worth setting LANG=C before running perl.