As others have said, if you bring the unit out of standby by pressing an input button on the MSR (which I think most people probably do) then that button determines which input is enabled in the unit. If you bring the unit out of standby by pressing the power button on the front panel, then I think the enabled input is defaulted to input 1 - I never do this, so I suppose it might also be last input used. I don't ever recall seeing a setting in mconfig to change this.

My Kit: 861v8+ID41, 800v4, UHD722, MD600, MS600, MS200, Oppo BDP-203, Genesis 201, Genesis 350 SE, Genesis S4-8 Sub, BG 520i, VTL MB450 II, Krell Showcase 7, Genesis 928 Subs, Danley DTS10 sub, SVS Ultra 16 subs.