There may be a bug here that needs extermination! I don't have experience with flags but I've used a method in EKOS to center a frame the way I want and it works repeatably over multiple nights - I pass this along only as a work around until the flags thing sorts out.

Using KStars or another planetarium package (I find Starry Night to be useful as well) I find a star at, or near, where I want the center of my frame. This works particularly well in areas like the Veil Nebula since there are stars everywhere. I simply use that star as my target and EKOS has framed things up the way I wanted. It survives meridian flips as well. I haven't tried it with a mosaic.

FWIW

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