You should already have signed a HUD form titled "For Your Protection,Get an Inspection." Do you recall seeing that form? If not, here's a link to it: http://24-7homefinder.com/newsimages/FHA%20HUD%20FORM.pdf. It's a very straightforward disclosure regarding the purchase of homes with an FHA loan, and the difference between an appraisal and an inspection. Best advice I could give you is to read this form carefully. Next step would be to discuss the situation with your Buyer's Agent. You do have one, don't you?
The appraiser's job is not to inspect the home as you may think of it only to note on the report that the home is in working order.
Appraisal determine value of home represents the lender.