When rebuilding index not every item indexed, or only partially
When I clear and rebuild the index in the preferences many items are not indexed, or are only partially indexed, but when I click the arrows next to "Indexed" property of the items they are usually index with no issues.
Why are you clearing and rebuilding the index? You should basically completely ignore that pane in normal usage (and it will likely be removed or buried in a future version).
The point is just that it doesn't index all of huge files by default, but if there's an individual file that you notice isn't being fully searched and want fully searched, you can click on it and index it fully.