It looks like the perl-gtk2-unique bug has been patched in Debian, Arch, will be fixed in the upcoming Ubuntu 18.04 and a report for Fedora 27 also exists. Therefore I think that the time has come to solemnly close it. Please open a new bug in case you are running a patched perl-gtk2-unique and still experience second instance crashes in Shutter.
It looks like the perl-gtk2-unique bug has been patched in Debian, Arch, will be fixed in the upcoming Ubuntu 18.04 and a report for Fedora 27 also exists. Therefore I think that the time has come to solemnly close it. Please open a new bug in case you are running a patched perl-gtk2-unique and still experience second instance crashes in Shutter.