I know nothing about Enigma Virtual Box and what it actually does to the game files... But what I can tell is that my plugin have been tested several times on deployed MV projects, both on PC and Mac, by me and many other users. And of course, saving game usually works (that's kind of the main feature of the plugin).
Beside, it's hard for me to tell what exactly happen here, cause even though my plugin heavily change the save scene and its behavior, when it come to actually save the game data, it use the default save methods of the core script...
What you could do first is providing a little more details about the 'bug', like you said save doesn't work; does the game crash on saving? Or it does like it is saving (playing the save sound and all), but doesn't change the save slot? Or it play the 'buzzer' sound when trying to save?
Also, you might want to try to delete my plugin from your project, deploy your project and turn it into .exe file with Virtual Box, and see if you can save a game file from the default scene.
I would like to help, but I'm kind of clueless right now...