I've got a very similar set up to yours and I'm having a similar problem. I've got a new Mac Pro (June), with an ATI Radeon 1900 XT, with 20" cinema and a Cintiq 21 UX. The 20" is my primary monitor.
At first start up (after being off for several hours, overnight usually) I'm getting a pyschedelic checkerboard of pixels instead of a grey screen on my cinema display. I can still see that the computer is booting up. After finishing the start-up, the cinema goes blue and the Cintiq finally turns on blue. After force shut down and restart everything starts up fine (at least so far it's always worked the second time.) I've also seen the screens with checkerboard pixels after waking up from sleep after a few hours.
The only hint of a solution I've gotten so far is what I have eliminated: it's not a loose video card, nor the power management or PRAM or anything solved by "repairing permissions" on my harddrive, or the Cintiq driver. But here's what did work: I unplugged the Cintiq (and an old Intuos 2 drawing pad) and start up proceeded just fine.
So I've been assuming the problem was with either the Intuos or the Cintiq, so:
I reattached the Cintiq (but not the Intuos) and I had good start-ups for about a week, then the problem started again, (now with just the Cintiq attached, no Intuos): but this time the distorted screens last through an other wise good start-up: that is, instead of empty blue screens at the end, I get a distorted version of my desktop (though all I can do is move the pixelated cursor around.)
I was on tech support with Wacom yesterday, and they helped me clean out some old versions of the Cintiq driver that persisted after I updated to the current driver. (Have you tried updating your driver?) The fellow thought that some how it might have been an issue with the old and new drivers interacting with each other after a period of time (???) As of this morning, this failed to resolve the issue, however. Anyway, he did seem doubtful that the external device (by which I guess he means the USB powering the tablet function of the Cintiq) would effect the start-up.
He did give me one fact that I'm thinking might be a hint at what's happening: He said that the cinema displays are so well designed to work with the macs, that they respond to a video signal much much faster than the Cintiq can, and this can mess things up: specifically the Cintiq will often have trouble waking from sleep.
There is a "mac sleep" mode you can set on the Cintiq (using the onscreen menus controlled on the upper right edge of the Cintiq), and this is supposed to resolve these issues (have you tried this?). It didn't do anything for me, but it may for you.
Anyway, I'm not sure if your seeing anything exactly like is happening with me, but you might definitely try setting your Cintiq to the "mac sleep mode" if you haven't done that yet.