I open Engineering and set the expansion to Khaz Algar and close the window. The next time I open Engineering, Khaz Algar is initially selected but within a few seconds, Classic Engineering is selected. This can be seen in the attached video.

If I select Dragon Isles and close the window, the next time Dragon Isles is initially selected then it switches to Classic Engineering. I did not record a video of this.

Note: I disabled Skillet and TSM to eliminate them as possible culprits. I do switch between Khaz Algar and Dragon Isles.

dont know if its maybe due to your classic favorit recipe?

I have been logging in and out of different characters and now logging into my Engineer, I can't get it to happen, with or without the favorite from Classic.

hm I remember once a user telling me a similar problem and then he stating that it was a different addon

craftsim has a "remember last recipe" option
maybe try if that is causing this?