I agree with the pp. It sounds like you won't be getting your refund until the IRS gets the answers they need.
Reason why letters like this go out:
Is anyone on your tax return in default of student loans?
Is anyone in arrears for child supports?
Any change that someone you claimed on your tax return was also claimed by someone else (i.e. a child claimed by an ex-spouse, etc.)?
Any chance you made an error on the tax return in regards to social security numbers, etc?