It isn't HUGE issue, but one I would love to fix none-the-less.
I run dual monitors, separate sizes and resolutions. Never been an issue as they run fine. My primary monitor is on an HDMI cable and my secondary is on a DVI cable. My issue is when my PC is asleep or off and I wake it up/turn it on. My secondary monitor is on instantly and my primary monitor flashes on and sleep mode about 10 times. Once it settles it is fine. It does the same thing when my PC goes to sleep after an hour of inactivity. The only diff is that when I wake it up after inactivity as opposed to turning on is that my taskbar and desktop icons are moved to the other monitor.
I do have my main monitor running through my Avermedia Live Gamer HD capture card, but it was doing this before I got the capture card.
Asus Maximus VI Hero
Nvidia GTX 770 4gb
Asus Xonar Phoebus
EVGA 1000w PSU
Avermedia Livegamer HD Capture Card
2xSamsung 840 Pro SSD's 512gb
4TB Western Digital Black HDD