So not only do you have to be in the window for your mount, but SGP has to call for it at the right time too. Do your SGP settings happen in this window?
Keep in mind you can test this during the day. Just make a new profile without platesolving, guiding or focusing. Then slew to a star within your window and tell SGP to perform a flip. If your settings are correct when you ask SGP to flip, it'll work automatically.
On my Gemini, I use my safety limits to tell how close I am to the flip and command the flip within 10 minutes of that number. I don't know if your mount gives you a read out like that?