I am having similar issues. The entire guide disappeared for about a week (posted up there ^). It then came back one night all of a sudden. Has been fine, but then last night it's gone again.
Question though - how are you manually running it to see progress? I've always thought it was a background thing?
If you open the TV server setup programme, look under the plugins section and then select the grabber there is a button on the first tab that says "grab now" - this will do a manual update of the channels, logos and epg and whilst its doing it any channel changes etc are also shown.