I have this bug as well. I’m on a Windows 10 64-bit, also with one 144hz monitor and one 60hz monitor.
Printing out delta time every update(), I noticed that it’s staying at 1/60 of a second, even on the 144hz monitor. The easy solution would be to have the delta time scale by 1/refresh_rate (ie. having 144fps). There are probably more refined solutions though.
I noticed another interesting thing about this bug: when you build to HTML Defold builds to a new tab in the latest selected window of your default browser, and whether the game is twice as fast or not depends on in which screen this window lies at the time of building. If you move the window over from one screen to the other after building the game speed won’t change. (using Chrome)