There's a good possibility that you or a tweak program you've used has disabled app notifications. Settings > System > Notifications and Actions.
I have mine disabled as well but, I still get tray notifications. I don't these settings will affect tray icons but, yeah, worth checking though.
Thanks again! This is indeed a wonderful program. My only note would be about the "Would you like to apply this image..." message, which is huge and kind of destroys the preview ability. It'd be nice if you could make it a bit less obtrusive, or make it disappear momentarily. The Advanced/Preview option doesn't work so well (it changes the aspect ratio).
Update: Code: Changelog 0.0.1.0: Updated Login User Picture Remover Added Lock Screen Preview Updated Message Dialog Minor Changes
I'd like an exact list of files or other changes this does to my system before I dare try it again. Last time (v0.6) I got greeted with a "Please choose boot device" on next restart and nothing short of a format and complete re-install of Win10 + applications would do. (tried everything except restore - I have a small ssd as system drive and don't have restore enabled on it) Windows10 Enterprise N LTSB x64 en-US (build 10240.16463.amd64fre.th1.150819-1946) What do I need to backup in order to restore the modified files from a bootdisk in case this happens again?