So I noticed that the "Send to.." menu in windows works fabulous and ShareX uploads the file to my server without mangling the name. So I'm guessing you're correct on the short name issue happening on SSCs end.
For the time being I've disabled the Upload with Uploader tool check box in the Post-Capture Options section of the Options dialog. For the time being I just use Keep image and then make any edits if I want. If I don't I just right click it in the explorer sidebar and do a "Send to..." and pick ShareX. With that disabled though it appears the ShareX image uploader tool in the red toolbox button doesn't work... (Which is why I have been using the Send To method.)
Anyway thought I'd report back with those couple of tidbits that I found.