When variable_dt is not checked the engine will rely on hardware vsync for each frame. The engine also assumes as a refresh rate of 60Hz.
With variable_dt checked the engine will update as fast as possible and calculate dt accordingly. This means that the size of dt can vary greatly between two frames which can be a problem for physics simulations for example.
From what is described in this thread and the fact that the issue seems to be isolated to Windows, there might be some precision issue with the dt calculation when running with variable_dt on Windows. Created issue DEF-3146 for this.
It is important to remember to use dt in your script update functions correctly. With variable_dt your update functions will most likely be called much more often, but with a smaller dt, than when running your game without variable_dt