Encrypting puts the graphics and data folders into the rgss3a file so they can't be accessed. That's just how the encrypting works.
Do you run the game.exe to pull the data out again before you put it to dropbox? Or do you put the game.exe itself onto dropbox?
Once you run that, you SHOULD be able to play the game, even though those folders aren't there, because they're embedded in that file. What DOES happen when you try to play the game?
Encrypt it, then run the Game.exe file to pull everything out again (but don't install it into your project folder). Leave dropbox out of it altogether (and any other folder that syncs online). Can you play it then?