I am still having this problem with the organism name rather than the hit name showing up in the details pane when connected to a Chado database. Again it is the two-level results.
This is with both the 1.11.1 release (post this bug fix I think) and with the latest code checked out from svn yesterday. The about box says:
'Apollo Genome Annotation and Curation Tool, version 1.11.1, last updated Nov 29 2009'
The problem also appears more serious than just the wrong name being displayed - if I select one of these features, right-click and choose 'Align Same Type Features In Region...' I get the organism names in the alignment viewer rather than the hit names and there is no sequence (i.e. it uses the genomic sequence). But the correct sequence appears to be there - if I select the feature, right-click and choose 'Sequence' I can see the correct sequence for the hit under 'Result Sequence'.
System information: apollo running on a variety of machines including Windows Vista, Windows XP and Ubuntu 9.04, chado running on a linux machine, postgres 8.2.
I haven't uploaded a chado dump as it's rather large but can supply one if need be.