An added sequence stops being reference in MSA

To reproduce the issue:

1. Open COI.aln
2. Open human_T1.fa
3. Drag the sequence to the alignment
4. Make the sequence reference
5. Change the highlighting mode to "Disagreements"
6. Use the dots
7. Drag the reference sequence in the list of sequences
   Expected result: the highlighting mode is the same, human_T1 is still the reference.
   Actual result: human_T1 is not highlighted as reference anymore, the highlighting mode is not applied (however, it is still selected on the Options Panel)