I have had exactly the same problem, and come to the same conclusion, i.e. closing SGP between creating each sequence was the only way I could find to avoid it.
This is how I would encounter the issue: I would open SGP, immediately go to Framing and Mosaic window, select and target, create a new sequence with it, save the sequence, close the sequence. Now if I go back into the Mosaic window and create another target and sequence, then save that new sequence, when I open the that sequence it has both target images associated with it. And if I keep doing this then I may have say 10 images associated. I tried deleting the unwanted images and resaving the sequence. But then when reopening the sequence, the associated image seemed to be a random selection from one of the previous ones.
This led to lots of deleting of sequences, starting again from scratch and closing SGP between target/sequence creations. That seemed to work fine.
By the way, the reason I am doing this is that I want to be able to create a number of targets. These might be just single framed portions of the sky. But I want to be able to create these at my leisure and then when I’m out imaging, then I can decide at the last minute what to image and create a sequence depending upon conditions etc. It would be great if framed targets (single frames or mosaics) could be saved separately to sequences. But maybe that’s going off topic!