We really can't help you with the small amount of info you have given. If you really want us to look at it, it might be easiest if you put white paper scraps over ALL identifying info (your name, address, SSN, etc.) on the notice AND your 1040, then scan them to a PDF file for us to see. (Or, if you have a nice PDF editor program, black out stuff on the scan and then re-PDF it.)
Check to make sure that you have all pages of your notice. Sometimes a later page will have information that helps explain what happened on the first page.
Check your files for other notices from the IRS. The IRS will apply your overpayment to any amounts owed for personal income tax from last year, other prior years, old penalties and interest from prior years, FICA owed (may be an issue if your are self-employed), and possibly other federal taxes owed, even if they are not income taxes. It is very likely that your refund was reduced for valid reasons, and it is not very likely (though possible) that the IRS has a math error. There is a chance that there is information missing from the notice as to how the "missing" money has been applied.
If you owed money from last year, remember that you would have interest AND PENALTIES. Also, those interest and penalty numbers keep adding up until you pay. If the last notice you got about them was old, the interest and penalties will have increased. If you owed money from last year and didn't set up a payment plan with the IRS, your interest and penalties will be pretty high.
What you have written is confusing, as you keep mentioning both state and federal amounts.
Just to clarify:
If you overpay one government entity and underpay another, the overpaid one doesn't send the overpayment to the underpaid one. So, if you overpaid the state, the state will return your money to you or apply it against other taxes for the state, but it will NOT send the money to the IRS.
If, after going through all your notices, you don't find the answer and still need to call the IRS, make sure you have all your notices in front of you. Having the notice numbers/your case number at hand, as well as all the calculations, will make it easier to know you are looking at the same thing as the IRS rep. I would suggest you make photocopies of your notices before you make the call. Then you can write all over the photocopies and take notes on what the rep says and still have the clean originals. You can also run through the list of notices for your SSN with the IRS and make sure that you are not missing any (through postal service error or a member of your family tossing the wrong envelope).