unable to reproduce this with Pd(vanilla) 0.48-1 and jackd-1.9.12 on Debian/buster+sid
confirmed with Pd-0.48.1 there are two problems: - Pd doesn't properly escape the quotes when sending the string to the Pd-gui (that's where you get your error) - Pd relies on the shell for parsing the quotes, so the option doesn't do what you want anyhow.
for bugs in the Debian package, please use Debian's bug-tracker: $ reportbug puredata apart from that, i cannot reproduce this myself. - which window-manager are you using? - did you tweak your window-manager, X11 settings,...?
section about cross-compiling Pd
Implemented "--sources" flag
more usage() and comments
remove build-artifacts in a case-insensitive way
strip files if requested