My first guess is that the game has plugins that are written in an older version of NW.js and the person's pc profile is on a newer version or vice-versa.
Mostly correct, but actually it's the version of NW.js that the RM game is using, and not related to the plugins itself.
Basically, it's kind of an error with the engine? Not even really that. It's a problem that happens for players who play a lot of RM games and it is a specific problem for the local machine, but may or may not affect other users.
Basically, when you play an RM game using the default version of NW.js that profile is saved to your local machine. Whenever you play an RM game where the dev may have updated the NW.js, that profile on your local machine gets updated with the new info.
Now, whenever you go and play another RM game that uses the old NW.js version, you will get this warning because it's not going to roll-back the profile saved on your machine.
@SGHarlekin had sent me a batch file that will bandaid fix this problem. I would send it here too, but obviously downloading random batch files from random internet users is not a good idea. Hopefully he can provide a source for where he got the file from (unless he programmed it himself

)