It's a side effect of the new start function that may happen on windows 10 systems when a controller is connected.
You'll be able to revert to the Fusion pause when 1.08 hits if that bothers you.
- Create a windows link to the game
- Right click on the link and select "Properties"
- Look for the "Destination" field, it contains the path of the application ("C:\BLAH BLA BLAH\Sonic3D2d 1.08.exe")
- Add the commands you want after the double quotes, separated by space ("C:\BLAH BLA BLAH\Sonic3D2d 1.08.exe" /MIS1 /OLDPAUSE /LIGHTWATER)
- Play the game from that link
You may still get slowdowns when levels load and you use a controller: it's windows 10's fault that for reasons out of my control takes a long time to load the controller's routines into the game's joystick controls.