Well, the checkbox you mention works like this:
When checked: Single regions will be saved as format 0, multiple regions as format 1
When unchecked: Always saved in format 1.
I’ve the newest version of Logic as well so according to your experience this issue is something from more recent versions unfortunately.
It’s indeed no problem when you import the MIDI file back in. It’s just that other MIDI players, including uTool, will show you a way to long MIDI-file time.
Normally the first track (tempo track) will be ignored so it will only count the actual MIDI tracks. But as Logic writes a whole bunch of tempo tracks with this 1 hour time it just uses this.
For now my workaround is that I import each Logic-exported MIDI in Pro-Tools First (free version) and save it without any editing from within Pro-Tools (select format 1). The MIDI file will now be correct (and will a fifth of the file size again).
I just can’t imagine Logic being faulty when exporting MIDI Format 1 so still looking into this problem.
I’m now planning to write a converter for this to skip the Pro-Tools part.