What printer are you using? I just tested that button with one of my printers and it correctly send "M18", which is the disable motor command for my firmware (see: http://reprap.org/wiki/G-code#M18:_Disa ... per_motors).
Of course, the commands may be different if you have a different firmware, but S3D will still send the right one if you have setup things properly for that printer (i.e. using the config assistant)
Why don't you post the communication log from both software programs. As I mentioned, the button is working fine here and sends the command I would expect it to. So open the software, connect to your printer, click disable motors a few times, and the copy the communication log. Do the same for your other software that works.
Perhaps you are sending different commands in one vs the other, but thankfully, you can easily change those things in S3D once you know what you want
I'm not sure why it would work fine for me though and not you. Seems pretty straight-forward
Yes... that's exactly what it's supposed to do. So again, if one is working an not the other, please post the communication log from BOTH programs so we can compare.