The answer to your question is "YES" the DMV or MVA is above the law, (at least in the state of Kansas). It is a Damn if you do Damn if you don't situation.
1. You test over the limit the DMV will suspend your license. (this is the DMV not the court)
2. You are found not guilty in court, the DMV will still keep your license suspended, because of a test failure. (the court and the DMV have nothing to do with each other in this situation)
3. You test over the limit and through an error or through an administrative hearing with the DMV your license is reinstated. If you go to court and are found guilty of DUI your license will in turn be resuspended by the DMV. (the DMV and the court are working together in this situation)
Like I said it is Damn if you do and Damn if you don't situation.
I believe this is a loophole for the DMV to keep you out of the drivers seat, because they know you were over the limit, even if you were through some kind of loophole found not guilty in court.
The only way for you to keep your license if you test over the limit is to not only be found not guilty in court, but to win an administrative hearing with the DMV. (which in your case is to late).
Kind of weird how our justice system works.
Like I stated this is how it is in Kansas, but from what I have read in this forum, it sounds like this is the law in many states or close to it.
Good luck to you!
Bini.
PS. Post back if you have any questions or do not undertand what I have stated.