We are also an FDIC regulated bank. I am not sure about the state in which you live, but in Oklahoma the FDIC trades off with the Oklahoma State Banking department to conduct Safety and Soundness audits every other exam. Therefore I know that they do care about internal audits. What they tend to review during their exam is the requirements imposed by your state banking rules. In my experience I have downright argued with them moreso over internal controls than over compliance issues simply because internal controls can be a gray area where regulations tend to be more black and white.
On top of that you may have an examiner that has a real beef about a particular control and want to write you up for it when they can't point to a state banking code that says you have to do it that way, but that they feel it would be "in our best interest" to do it their way.
As far as the mail room, you could say that there is a risk associated with deposits or loan payments coming in through the mail. Are these being opened under dual control? How are they being logged? It is a risk, it is how you forsee that risk being detrimental to your bank that tells you whether or not you should audit that type of an operation.
Here is a link to the FDIC's Safety & Soundness examination manual. This should guide you to what they would review during their examination so maybe you could gear an audit program to that. http://www.fdic.gov/regulations/safety/manual/index.html