Another possible cause of the problem is that you're recording one of the stations that just seems to flummox the iView. Ion affiliates are particularly bad about this, but I've seen it on others as well.
Many stations will cause the iView to "double-clutch" when you tune them: the station tunes in, but then the screen goes blank for a second and then the station tunes in again. Usually that's just a minor annoyance, but a few stations seem to go further: the station seems to get completely erased and added back. Any subchannels you deleted, renamed, or skipped suddenly reappear and go back to their original names. If this happens, I suspect you'd lose any timers you've set for the station as well.
I don't know of any sure cure for this. Leaving the iView turned on and tuned to the station in question may help, but even that's not guaranteed.