You're doing the same thing my Aunt was doing for her Love it or List it Habit. I got her to change to setting timers differently, and she likes it better: Always et SERIES timers (New or New and Repeats) NOT one-time timers:
1. Hopper will automatically handle conflicts such as when a show airs more than once on the same day or more than one in the same week. For example, if there is a conflict and no tuners available for the first airing of that episode, the DVR will automatically record the very NEXT showing of the same episode, often just 3 hours later. This also applies if the episode won't be repeated until a few day. It will NOT record any recordings you already have (sometimes I think it does) and does all this automatically. Setting ONE-TIME timers will make a mess of trying to record what everyone wants. If your wife doesn't want to wait until the next showing 3 hours later, than she can place her Series timer at the higher priority. In that case she get her show recorded first, and the other shows get recorded later.
2. Often people who set one-time timers like you wife, often record what they already have recorded on the DVR or record an episode they have already seen. On a SERIES Timer, there will be an red X on the guide for that show meaning that she already has recorded on the DVR for New and Rerun timer or it is not NEW for the Only New timer. No sucking up timers just because she THINKS she hasn't seen it just want to go hog wild. The DVR is doing all that work for you. Otherwise, she is gonna suck up tuners unnecessarily. The hopper can manage that far better automatically. If she is afraid of having not seen a show, then she can set her SERIES timer for New and Reruns, then she won't miss any old ones she has not see.
Believe me. Simplify your life. One-time timers, unless set to the wee hours, is just an unnecessary frustration like you are experiencing. By the way, it makes no difference which timers does the recording. They are colored for us just to know at a glance that we have ONE or TWO or THREE things recording at that time. It is all automated and trying to always have a particular timer you prefer to record is just not how it is designed or necessary. Good luck.