@Mr Crash: I'm not positive but I think maybe the javascript isn't loading correctly when the control is "totally broken" (missing the controls at the top). If you do a hard refresh (hold down shift and click refresh) on the page, do the controls eventually show up sometimes or are they always gone?
The control works like this - we put a normal <textbox /> in the source and apply a class to it. There is a javascript that runs on page load that goes and looks for textboxes with that particular class attached to them and then initializes the TinyMCE control. The TinyMCE code hides the original textbox and spawns a bunch of new html including a table containing the toolbar and an iframe which is where you actually end up typing into. The first image you posted makes me think there is somehow a negative css margin being applied to the content inside the iframe. The second image makes me think the javascript never loaded that makes all the TinyMCE "magic" happen. In Firefox, if you right-click on the textbox when there is no toolbar (ie: "totally broken") and click "Inspect Element", my guess is that it is just the normal <textbox />. Otherwise, you'd see an <html /> element inside an <iframe />.
When I said we've been in contact with TinyMCE, that probably did sound vague but not because I'm trying to be political but because I'm not the particular developer who contacted them or have been working on it 
I remember Geoff mentioning he had either emailed someone at TinyMCE or filed a bug but I'm not sure what the outcome was. I just replied to you because he was on break for the week and I didn't want you to think the problem was being ignored.
Anyway, the other day after we spoke about this, I downloaded a new, untouched version of TinyMCE and I did not see the strange focus issues in IE9 out of the box that we are seeing on our site so I tend to think the problem is on our side somewhere. Could be a stylesheet issue, could be some of our other javascript not playing nicely. We have a "theme" that is being applied which contains our C9 emoticons and who knows what else that may be causing the issue as well. Geoff, who just got back from a lovely break, is working on it as we speak and I think he may have less hair now than when he started 
Can you do me a favor and look at the example on the TinyMCE site (link below) in Firefox and IE and tell me if you're having any of the same problems with those examples? I'm mostly curious about the negative margin and no toolbar issue that you posted the images about since I haven't heard of anyone else having those issues.
