I noticed that I am missing 11 resources, all seem to be different versions of the Bible. i.e. ESV, NIV, NASB and such. Any clues as to where these may have gone?
Sounds like these are interlinear bibles. I know we updated these recently. Have you tried running "Update resources"? Do you have "Automatically Download Updates" set to "Yes" in your Program Settings?
If you have and still haven't been able to get them, it could be that the indexer is trying to download them but encountering a problem.
Posting your logs will probably help. Please see the FAQ link in my signature, item #6 for more information on how to post your logs.