I looked closer at the log file and see that what was happening is the first 93 users it processed had an error of "Unable find mailbox timezone". Yet, it put those users in the output.txt and most of them had a timezone listed for them. After the first 93 users, though, all of the users had the error of "Unable log onto user mailbox". This was all done with version 1 of the tool as I was running it from the MS supplied virtual machine. I've since created my own virtual machine with version 2 of the tool. So far the extraction is showing the "Unable find mailbox timezone" error for each user (including those that exclusively use OWA). I am seeing the occasional "unable log on to user" but it doesn't appear to be as much as before.
The problem I'm having with THIS install though, is that if I try to apply the hotfix from last weekend (KB933146) it fails. No error or reason, just "The update failed". Is this update Outlook 2007 specific because this machine has Outlook 2003 installed on it. We don't have 2007 here...