I reinstalled Logos after wiping my laptop's hard drive and starting over. I decided to install the beta from scratch.
The installation seemed to proceed normally, after the files downloaded it indexed and appeared to complete normally. While the indexer was running I ran the javascript to enable logging. When indexing was done I closed Logos and did something else. When I restarted Logos it found ~200MB of files to download and then started to index again without restarting. When I looked at the homepage it told me that first time indexing was running. So, I peaked at the log files and evidently the first index was corrupt and Logos was redoing the whole thing.
When it was done the Logos icon in the system tray invited me to restart Logos to install the resources. I closed Logos so that I would have time to save the indexer log and grab the 2nd one in case something interesting was in it. However, after I started Logos there was no resource discovery and no indexing. That 200MB I downloaded seems to have disappeared.
Weird.
Here's the one indexer log I got: 7288.Logos4Indexer.log