Further research reveals that although Hijack cannot find the script in /usr/local/bin (so I have to specify the full path in config.ini) it does seem to find rsync which is in /usr/bin. So there does seem to be a default path set somewhere, although it doesn't get it from /etc/profile.

I've also determined that the script gets as far as running rsync, but which never finishes. If I manually kill rsync from the commandline the script continues as it should.

Why would rsync be getting stuck like this?

Could it be a display problem? I'm using Pim's rsync that displays progress on the VFD. But does Hijack grab that for the menu display? Would that cause rsync to halt?