This is not a new bug, but I don't think it's been posted before. Under certain circumstances, it's possible for the indexing icon to get confused as to whether it's supposed to be indexing or not. The screenshot shows a grey icon, but an indexing tooltip, and the logs show this:
2011-06-16 11:05:17.7774 1 Info WindowsIndexerProgram Setting notification icon tool tip to: Logos Bible Software is indexing (28% complete)
2011-06-16 11:05:19.5646 1 Info WindowsIndexerProgram Setting notification icon tool tip to: Logos Bible Software indexing will resume in 3:11
2011-06-16 11:05:32.7799 1 Info WindowsIndexerProgram Setting notification icon tool tip to: Logos Bible Software is indexing (29% complete)
2011-06-16 11:06:19.5816 1 Info WindowsIndexerProgram Setting notification icon tool tip to: Logos Bible Software indexing will resume in 3:10
2011-06-16 11:06:32.8139 1 Info WindowsIndexerProgram Setting notification icon tool tip to: Logos Bible Software is indexing (30% complete)
0677.Logos4Indexer.log
The particular circumstances that create this I'm not entirely sure, but I think it happens when you download something whilst indexing, then pause the indexing, then restart Logos after the download finishes. You seem to end up with two indexing operations, the first one (paused), and the second one (active).
