When I have this option on
Then this option stops working
Works OK here, at least when setting the background event to run Help ABOUT.
hmmm - one of those 'only happens to me' things then 
Did you try using a simple command instead of the usercommand/script?
works, then switched back to script and it now works.
But I've had this problem before and have had to switch off 
when it stops working.
If it stops working again, please do a config backup before & after changing that option, and email those to us. Comparing those might reveal what happened, or at least why changing that option fixed it.
(We can probably narrow it down to a single config file, if you don't want to send whole backups. If you make backups normally, it's possible to get the single fife out of them, which I can explain in detail if needed, if it happens again.)
found a bckup where it is not working, will send 2 backups - id 343
(will have to change the above setting to on)
The setting is already off in the older backup. If I turn it on, save, then off again and save, the config is identical to how it started.
Toggling it the opposite way (off, then on again) in the newer backup also results in a config that's identical to how it was started.
Middle mouse works OK for me in both backups, opening the custom menu.