view pairwise alignment in alignment editor shows two copies of one sequence

The new version of the pairwise alignment view implemented in JAL-207 is buggy:

Import:
>a
asasasasasasad
>b
dddasasasasddd

Select both sequences, perform Calculate->Pairwise alignments... and then hit 'View in alignment window'
In the desktop, the alignment contains sequence 'a' twice.