I've come across this issue and was wondering if it could be a bug, I've prepared a small demo, check the .capx.
Basically, if 2 objects are already making contact, disabling collisions won't affect them.
Anyway, here's the capx: http://dl.dropbox.com/u/1910765/bugtest.capx
As you can see, if you disable collisions when the 2 objects are already making contact, the first object will stay there instead of falling down.
Hope it helps. Thank you.