I only know that it happens when the display scaling of the browser and Windows desktop don't match, for example my Windows setting was 125% and the problem went away when I changed it to 100% (which makes the fonts on this computer uselessly tiny but popups worked!!)
I bet if you look carefully at what's happening with your VPN there is some other issue involving display scales, like there's Remote Desktop Connection or Citrix or something like that that is running in a scaled window?? Is this possible?? Or you're running a browser on a remote system and its scaling is different?
If that's the case then yes, updating the JSAPI should fix it!