That is interesting. Just speculation, but I do know there are several different levels (and thus types) of sleep, so perhaps the manual sleep is invoking a different level of sleep than the automatic one.
You could email Matias. I find that they are very responsive (in my limited experience).
Just to add to the discussion, my mouse's logo illumination can be configured to cut the illumination (or pulse it), based off of several things like computer sleep or even just monitor sleep (where the computer is still on, but the screen has gone into power saving mode).