You may notice when you go into the timer menu that the event in question appears in the wrong place in the listing, this is a clue that the event was mis-filed. Example a weekly timer set for Saturday is grouped in the section with the Sunday events. Try removing the event a re-add it again, that had worked for me.
As far as channels appearing red in the guide that shouldn't be, this happened twice in one particular week. It occurred in the days following the time I had my 921 replacement. The first time it was fixed after a re-boot and the second (day or two later) I had to call dish. My feelings is it something DN caused and as you pointed out, occurring just after an audit may be a simular situation as my new replacement was. Once DN got my R00 and S00 numbers for the final time I haven't had that occur.