The inotify handle is gotten when you set the output->permanent-file.
If you clobber the output file then maybe that's tripping up the GUI.
Wireshark should get inotify handle of the File->open pcap or the as put on the wireshark /tmp/my.pcap commpand line.
But it doesn't seem to. Instead the workaround is to use the File->Open Recent shortcut. i.e. press "THE MICROSOFT WINDOWS START KEY" and 0.