"Watching" does not affect timers on my system. My tuner Status page almost always shows the Hopper "watching" on two tuners while the Joey is "watching" on one tuner, the exception would be when the Hopper and/or Joey are watching a recorded event. If one timer is activated, it grabs a tuner, this is typically the secondary channel allocated to the Hopper. If a second timer is simultaneously activated, it grabs a second tuner, typically from the Joey. The Joey then goes to the tuner status page so that you can choose to go OnDemand, to DVR, or share the remaining tuner with the hopper.
I have only had one conflict in the past week, and in that case, all three tuners were actively recording.
What I'm trying to say is that your Hopper "watching" two tuners is not likely the cause of your timer problem. It is normal for the Hopper to watch two.