Your second log file there Patrik suggests that the tracker-indexer is
not running or is not responding - this probable explains why you see no
more index error notifications. So, I'm ot yet convinced that it is
fixed for you, and I think I understand the issue here.
** Changed in: tracker (Ubuntu Jaunty)
Status: Fix Committed => In Progress
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Tracker uses notifications with actions when the index is corrupt
https://bugs.launchpad.net/bugs/361205
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