I only really notice it when I get home from work because I am flying the entire time I'm at work, so I've usually gotten on a plane back to Torn by the time I'm getting home. The PC the script is on boots up to me being mid-flight back. When just the PC is the one doing the flying, the script works flawlessly.
Once I've gotten back to Torn, I will test it out when trying to load the script from being closed entirely while mid-flight from Torn to Mexico to see if the problem only shows when on return trips.
After trying a few times, it didn't seem to matter whether I was traveling to or from Torn, I needed to initiate the flight with the script enabled to get it to notice I am flying on the main flight tab.
I've been testing and can't reproduce your issue at the moment. Can you let me know your setup: OS, browser, tampermonkey version, script version. I think you said desktop. Just to get more of a background on how you're running it.