I use trigger output 1 of the 990 to turn on the switched outlets of my power center. Connected to the switched outlets are a 5 channel amp and subwoofer for my main room. I was expecting the trigger output to only be active when Zone 1 was active. Nope. I just hooked up Zone 2 and when only Zone 2 is on, my amp and subwoofer in the main room also kick on. Has anyone else encountered this issue and find it annoying?

Yep, I was annoyed by the same exact thing. There is an easy work-around. I found no reason for my amp to be on in zone 1 when the only thing I had running was zone 2. So, I hooked up my amp to assignable trigger 2 and assigned every possible input to turn on trigger 2. Therefore, any time I have any input selected in zone 1, the amp automatically turns on. Turn off zone 1 (i.e.-no input selected), the amp turns off.
Hope that helps.

Sweet, thanks! That works great.

Now, is there a way to change the radio station from Zone 2 when Zone 1 is off?

I'm afraid that changing the radio station requires having zone 1 on.