Right clicking on the employee/Shift record in conflict and selecting display conflicts should show what subset selected the records first.  If there is no information indicating what subset selected the employees records first or it is the same subset you are currently running, you may need to reset the conflicts manually.

To do this, first Reset ALL Subsets, do not allow anyone to run select and edit again after doing this.  

After resetting all subsets ensure the ISTPCy/STPCNF and ISTPCy/STPSET files are empty.  If not, clear the files.

Re-run select and edit to ensure conflict is gone.