Did you do a clean uninstall of 3.3.2 or whatever that earlier version was. Don't even try with anything other than 3.6.1 WS installer as it wont work (different EUCON) even if it does show up.
Clean EUCON Script
On the SC264, when you say clean install was that after uninstalling eMix and then the Hybrid App. If you back up titles etc. you could then delete the eMix directory. (but you shouldn't need to, all others using this software are connecting OK)