FHA loans are very commonplace these days. They are about all that's left for people with little or no downpayment. Years ago, the FHA inspection killed deals but they have very workable inspections nowadays.
It is my understanding that all downpayment assistance programs will be gone as of October 1st. Maybe you can get this deal done under the wire.
The 6% is probably 3% for downpayment and the 3% for closing costs. (Just a guess)
FHA requires 2.5%- 3% for downpayment.
Closing costs are things like: Whole House Inspection, Radon Inspection, Wood Boring Insect Inspection, Tax for 3 or 6 months held in reserve, Insurance for 3 or 6 or 12 months held in reserve, Mortgage Insurance, Commission, Recording Fees, Document processing fees, etc.
I can't see your paperwork from here so it's difficult to know exactly what is going on but I don't understand why your agent can't answer the questions you have. Ask her to consult with her broker or call her mortgage lender contact. Surely there is a realtor in her office who can help figure this out.