That's strange indeed.
Is it possible to see and copy individual files from the joiplay save folder?
If you managed to copy your latest .save file and the persistent save file to your PC, you could just copy those into the saves folder of your PC version.
Also, make sure that the save folder isn't just in a different subfolder or named anything different than 'saves'.
If a folder with savegames is there, but not exactly in the right place and with the right folder name, the game may not recognize it.