Hey so I actually found a rudimentary solution to this bug recently and thought I'd share it. It seems sprytile has a hard time locating the original png when attempting to load tileset on any mesh which has been already created, as I learned when i attempted to reorganize my whole project and suddenly none of my tilesets were loading. After stressing out for a minute about this, I found that if I decided to add tileset rather than load tileset it would actually continue to allow me to paint on the object. Unfortunately this creates a duplicate tileset in blenders data every time I do it, but that's not a huge deal all things considered.
I also wanna thank you for making such an incredible tool for blender ! I am currently working on a demo level for a game I am creating using sprytile heavily... I don't know what I would have done without it, you are seriously the absolute OG Jeiel Aranal! Thank you so much for your efforts.