auto calculated alignment annotation rows do not get placed above or below non-autocalculated rows

The alignment annotation ordering options in the UI allow the order of display of per-sequence annotation and autocalculated annotation shown in the alignment annotation area of the alignment window.

Currently, specifying 'Show First' or 'Show Last' only reorders the autocalculated annotation with respect to the sequence associated annotation. Any manual tracks (non-sequence asociated and non-autocalculated) seem to stay where they are, so 'Show First' and 'Show Last' do not reorder the autocalculated annotation rows with respect to manual tracks.

Reproduce by:
Import RF00031_folded.stk and display the secondary structure annotation row for the first sequence, in addition to making sure the strucConsensus and Consensus rows are visible.
Drag the *alignment* secondary structure annotation to the bottom of the annotation panel and try to change the Show First/Show Last settings - observe that the alignment associated annotation remains at the bottom w.r.t. the autocalculated annotation.