Annotation tracks displayed on top of each other after 'Add reference annotations'

Import two structures for this alignment:
>FER2_ARATH/1-148 Ferredoxin-1, chloroplast precursor
MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
TIETHKEEDIV--
>FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor
MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE
VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV
VIETHKEEELTGA

Select both sequences, discover and open structures via structure chooser, then with the selection active, try 'Add reference annotation' - the annotation tracks are shown piled on top of eachother.

This is a regression from 2.11.3.0