Wait.. isnt this happening for everyone? I thought the devs would be aware of this.

You select a file, press the up arrow, it moves the file or packet up and then "looses" the marked state for that item. Here is the log part for this:

20-Mar-2009 02:45:34 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(moveSelectedItems)] -> 0 - 1
20-Mar-2009 02:45:34 - FINER [jd.controlling.interaction.Interaction(handleInteraction)] -> Interaction start: Trigger: Linklist structure changed
20-Mar-2009 02:45:34 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable$2(actionPerformed)] -> REFRESH
20-Mar-2009 02:45:35 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(fireTableChanged)] -> REFRESH GUI COMPLETE
20-Mar-2009 02:45:35 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(moveSelectedItems)] -> 0 - 0
20-Mar-2009 02:46:01 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(moveSelectedItems)] -> 0 - 1
20-Mar-2009 02:46:01 - FINER [jd.controlling.interaction.Interaction(handleInteraction)] -> Interaction start: Trigger: Linklist structure changed
20-Mar-2009 02:46:01 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable$2(actionPerformed)] -> REFRESH
20-Mar-2009 02:46:02 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(fireTableChanged)] -> REFRESH GUI COMPLETE
20-Mar-2009 02:46:02 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(moveSelectedItems)] -> 0 - 0
20-Mar-2009 02:46:02 - INFO [jd.gui.skins.simple.components.treetable.DownloadTreeTable(moveSelectedItems)] -> 0 - 0

So I guess the "Refresh Gui" is causing the loss of the marked state for the item. I marked a file, pressed up twice (only of of which worked) and than marked another item and pressed up twice again.