I think that I found a problem in the sequence editor: if you create a sequence with Fits file reference for coordinate for the first target and with no fits file for a second target, but explicit coordinate, after saving and opening again the sequence file, the second target slew to the .fits position of the first target, ruining the sequence.
Step to reproduce:
Create a sequence with a first target with any sequence.
Fill the FITS field with an existing file.
Apply job changes
Clear the FITS field, load the coordinates fields with the actual position of the Kstars
Create a new target with the "+"
Select the two target and verify that the fields are correct (FITS field is filled only for the first target)
Save the sequence with a "test1" name
Check with an editor that the file test1.esl contains the FITS keyword only in the first target
Load the "test1"
Now the FITS file name is present in both target.
Save with a "test2" file name
The FITS file name is now present in both target also on file.

If you run that sequence, on the second target, the mount will slew first to the explicit coordinates, align, and then solve and slew on the FITS coordinates.
Let me know if I'm doing something wrong, I'm quite new of the Kstar/Ekos environment.
(Ive the logs and analyze files available, if needed)

Thanks
Paolo