I have encountered this problem a couple of times and don't know if this has fixed it but once I started doing it I did not have this happen again.
I have been shooting a 10 second frame and focus shot from the home position when I start and then plate solve it. I don't tell it to save as my target I just do the plate solve thinking that maybe it lets SGP know where it is pointed. After that I start the sequence and it finds it's target.
Like I said this might just be bogus but since I started doing this I have not had it happen again.
Lastly because of that whenever I change to a different target I go back to home and repeat the process.
Sounds more like superstition than science but for whatever reason I am not dealing with the issue anymore.