I just tried again using the illuminated button inside the boot lid. I got the double beep again. It works fine from the remote though. It does not appear to be a glitch.

 

I think it's meant to be that way. On keyless entry it checks to make sure the keys aren't in the trunk before it closes with the button. So you don't lock the keys in the car...
If you disable keyless entry it can't tell if the keys are in the car. So the trunk won't close unless you use the fob button (as then you know the keys aren't in the car)

 

That's odd, mine works flawlessly unless something stops it. Might be different functions between models, seems strange tho