TJH, I have had similar problems to you in the past. I think your CM15A is crapping out. They only seem to last a certain number of years before they start behaving weirdly. I have had to replace units in the past that began to malfunction. Over the years, I think I bought 6-8 units.
I still have 3 units. Two of them known to be working properly, one is questionable. I'm starting to look at an Ocelot or ISY controller but would rather stay with Activehome if I can.
Tom G.
I was noticing a similar thing with my own CM15A skipping a few timers over the past few weeks. I added a few extra timers in there to cover the most important things, but I was wondering what was going on. It had also tried clearing the interface and re-downloading. This morning, I went in to look at the Dusk/Dawn settings (unrelated to the other issue), and I noticed that the battery life was showing as "red," but 48 hours. Resetting it didn't help at all.
So, I unplugged the CM15A, and opened the battery compartment. The batteries had leaked (I don't think they were all that old - I thought I'd changed them over the summer after our extended power outage). I cleaned off the contacts and replaced the batteries, but AHP didn't reset the indicator to "green."
I pulled out one of my spare units (I have about 5 total), and it also had a little corrosion on the battery terminals. Cleaning it didn't make a difference, it also showed "red." I tried a third unit, and it was fine (it showed up "green). That told me the software seemed to be okay.
Next, I went back and scraped the contacts in that second unit again, and it decided to work, too. Finally, I gave the contacts in my original unit one more cleaning, and it finally worked. I can't say the two are related, but perhaps the battery status was interfering with the timer operation in some way. With dirty contacts, the CM15A wasn't seeing the batteries at all.