About 50% of the time when using the remote to say "yes" or "no" , the remote will actually move the tv guide behind. This then means the pop up box is stuck permanently in foreground and cannot be changed
Is this with using any BlueTwo skin to test.
MEDIAPORTAL - free MediaCenter HTPC Software - MpTrayMod
If you have a mce remote, may help with the focus issue.
Still looking at your logs, but the error log has something i cannot pin down to anything i know of being the cause.