Doug, TIA's post might not have made sense literally, because it left the reader to read between the lines. Let me, if I may, reiterate it in a way that you may understand better.

A legal finding in your favor does not necessarily mean that you are not guilty of the wrongdoing with which you are charged. Plenty of innocent people have been railroaded, and plenty of guilty people have gotten away with their crimes. In the US, if you are white, male, and your father is a congressman, or if you are a famous celebrity with millions of dollars, you are more likely to get away with your crimes. Many people believe that OJ Simpson was guilty despite having gotten a Not Guilty verdict. In the same way, Bush could be guilty and never even charged with wrongdoing.

The point is, the fact that Bush was never disciplined is not proof that he never did the crime.

Clint's point above is also important. In military organizations in particular, where strict adherence to regulations can make or break a career, and where a chain of command is expected to enforce discipline, there is strong pressure, and a documented tendency, for those in authority to "look the other way" when crimes occur. They cannot have occurred, the argument goes, because if they had it would mean that regulations were violated, and that the entire chain of command was guilty of poor discipline. Thus, if a CO charged Bush with going AWOL he would also be charging himself with allowing it to happen. When ordinary soldiers or airmen go AWOL, this is no big deal because nobody pays attention. The CO can charge them and no one asks questions about the chain of command. But charging a congressman's son ensures a certain degree of publicity that can only reflect badly on the CO. It also ensures the enmity of of a Congressman, who may ultimately pull strings and use the bad publicity against the CO. It would be easy in this case to let Bush slide.

One final point. You can indeed go AWOL and still get an honorable discharge. One of my friends went AWOL from the Navy and was given the option of an "other than honorable" or of making up extra time in the service and getting the "honorable." Since there are no records of Bush in Alabama at all, he could have been kept on the books an extra year after going AWOL.