I have installed none of the upgrades and Zone 2 alone works fine either with the main on or off. I was able to turn on Zone 2 without the main being on.

I'm a bit confused though, do you have trigger 1 running to the 7125?

I wonder if it has something to do with using the two "open" channels on the 7125 as a Zone 2 amp. I run a separate amp for my Zone 2.
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Outlaw 990/7700
SVS 20-39 PC +
SVS MTS-01 towers, MCS-01 center, MBS-01 surrounds
Behringer A500
Samsung PN58A650, DirecTV HR-20 700
Sony CDP-545, Phillips CDR 765
Oppo BDP-93, Panasonic DMR E515
Technics SL-DL5
Squeezebox 3
Remote Harmony One