If you ran a defrag (via eseutil I assume), then you should also run isinteg. Although eseutil is handy for cleaning out an infostore, it does not see infostore databases as Exchange Server databases. There may still be a bunch of errors in your infostore file. And it will cause weird stuff like blank folder, non-existant emails. Blank emails. folders linked in the wrong place, etc.
1. Rule is always have a backup of your infostore, but I know sometimes that is not always reality. Anyway whenever I do a defrag on an Exchange server I also finish it off with isinteg. This is the command I run:
From C:\program files\exchsrvr\bin:
isinteg -s <servername> -fix -test alltests
It will prompt you on which infostore you want to run the utility. And you should have the store dismounted.
Also when it runs through the test be sure to verify if there were errors or not. If there are errors I keep re-running isinteg until there are no more errors reported.
Hope this helps.
P.S. Get a backup first. I have never lost a store doing this, but well, you know...