Chris Yep and I spent a bit of time last night on this one (I appreciate his time on this). Attached is a sample MAT file. Import it into GnuBG. Set your analysis options to expert/expert (Although other levels will likely show same thing). Now click move 61:bar/18 in the move list. Click on Analyse menu/Analyse move. Look in the analysis pane. You should see 3 candidate moves. Often the users selection loses its highlight, as well the moves are listed as 1,2,-1 (Not 1,2,3). If you click on another move and then go back to this analysed move the output is correct (And the highlight appears).
After some discovery I have found you can pretty much reproduce this bug on many positions where the user makes the worst move possible (And falls at the bottom of the list) and then you do an analysis. Sometimes what will happen is that when analysed the worst move will be sorted improperly and the move appears in the analysis pane out of order (but with the correct equities).
bug3.mat
Description: Binary data
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