I don't know if you're still updating this, but the custom tile function is not working for me. Is it a bug or am I doing something wrong?
Viewing post in Sidescroller Tile Set Maker comments
Honestly, I'm not sure where the issue lies. I have taken your image and tested it with STSM and I get this much more sensible result.
I would recommend you use this slope, STSM cannot deal with overhangs but I cannot guarantee that it will fix your issue.
I assume you're already using the most recent version of the tool? If not, download it again.