If you go to your SOUND panel under control panel you will find the SOUNDs assigned to different things. For example the sound when you minimize a window, or get a email, etc. Just because it 'sounds like Skype' doesn't mean it is EXCLUSIVE to Skype alone that uses that sound. Any 'action' can be assigned the sound.
Also secondary to that, have you considered making sure your PHONE also has skype removed? I know I turned off the computer one night and kept hearing the sound, forgotten I had SKYPE NOTIFICATIONS turned on my phone. Confused me for a few minutes till I looked at my phone - LOL!