Desktop comes up on 2nd monitor before showing up on Primary Display.

12 core mid 2010 macpro.  My First monitor is a cinema display connected to DVI connecter on the ATI HD 5870 card and my 2nd monitor is hooked up via the first adjacent mini-display port (with an hdmi dongle).  All works well except on boot, even though the display prefs are set so that the 30" cinema display is the primary one, the entire desktop shows up on the 2nd display for a moment and then after a "Blue Blink" everything shows up again on the primary monitor.  The issue is that all of the items on the desktop are an utter mess.  I also notice in the about this mac info pane (on displays) the HDMI connection is listed first, the Cinema HD display 2nd.  Is this a bug?  It seems to me that once you set the display priorities in the display preference pane the machine should be able to get it right the first time.  Is there something else I need to set or is this something I have to live with. 

Not sure what you mean about "display priorities".  Where you plug these guys into your video card is immaterial.
Did you define the 30" as the "main monitor", i.e., the one containing the menu bar?   Look at your Displays preferences, Arrangement tab.  If the little white menu bar is not on your 30" drag it there.  That is then where your boot displays should show. 
It wouldn't hurt to click the detect displays button the displays preferences and also do a smc and pram reset.
...the entire desktop shows up on the 2nd display for a moment and then after a "Blue Blink" everything shows up again on the primary monitor.  The issue is that all of the items on the desktop are an utter mess.
What this sounds like to me is that for some reason when you desktop is coming up after logging in is that the "other" monitor is where it is being drawn, and then the 30" is enabled, made the main monitor, but the resolutions got screwed up in the switching, and that screwed up the icon and window layout.  If I didn't know better it sounds like you are using SwitchResX and don't have it configured correctly.  I say that because I believe I could simulate what you describe by setting up SwitchResX to do that. 
Currently I have 3 monitors attached to my system.  One is for the TV and defaulted to be disabled using SwitchResX.  When I log in I also get that "blue flash" but that is SwitchResX setting up my default monitor configuration as it disables the TV connection (SwitchResX is a login item).  But since I have a proper SwitchResX configuration my primary monitor (27") and my secondary monitor (VGA) come up properly (after the flash).  But it's that flash you describe that made me think of SwitchResX.
As for the System Profiler displays information, I don't know what order it decides to list that stuff.  But I don't think it has anything to do with a "priority".

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