are you seeing any data in the mp_TaskQueue and mp_IndexingQueue tables?
Can you verify that in mp_Sites the SiteGuid field is not an empty guid?
I've seen in some installations where there is a problem with file system permissions for XmlSerialization, because it compiles temporary files down under Windows\Temp.
You can configure t to compile them in a site local folder but you need to know the file system path. If you look in Web.config near the bottom you will see it commented out:
<!-- the below example can be useful if you encounter the error described in this post
http://www.mojoportal.com/Forums/Thread.aspx?thread=6741&mid=34&pageid=5&ItemID=3&pagenumber=1#post27613
-->
<!--
<system.xml.serialization>
<xmlSerializer tempFilesLocation="D:\__projects\mojoportal\__code\joedev\Web\Data"/>
</system.xml.serialization>
-->
you could try un-commenting it if you know the file system path that maps to /Data
XmlSerialization is used to serialize the task and the index items into the database.
Hope it helps,
Joe