One PM is over billing me that I have to resolve and one is charging a prepaid fee to the tenant for furnace filters.  

That is where they put in there fees (points, prepaid interest, etc).2. taxes, title fees, state fees3. if they are only lending up to a certain % of the ARV, then you most likely are responsible for the difference between the overall costs (purch, repairs, closing costs) and their loan value.Like I said, without seeing their info I can't tell if that is the reason or not, but my guess is that is why it is so high.

Any payments on the balance remaining from the original loan must be included in the debt-to-income ratio calculation for the refinance transaction.Note: Funds received as gifts and used to purchase the property may not be reimbursed with proceeds of the new mortgage loan.The new loan amount can be no more than the actual documented amount of the borrower's initial investment in purchasing the property plus the financing of closing costs, prepaid fees, and points on the new mortgage loan (subject to the maximum LTV, CLTV, and HCLTV ratios for the cash-out transaction based on the current appraised value).All other cash-out refinance eligibility requirements are met.

What do you mean by pre-paids?

You should get your money back and then move on - application fees/credit checks, any deposits, prepaid rent, etc...

Simply put, points are prepaid interest on the loan.

I'll give you a quick run down on the closing costs from a duplex I purchased for 250K:Loan origination charge: $750 (this may be 1% of the PP, however we went through a credit union on this one)Appraisal fee: $275 (I've seen this fee go closer to $600 on some purchases )Credit Report: $11Tax Service Fee: $70Flood Cert: $9Title Services and Lenders Title Insurance: $1,520Owners Title insurance: $271Government Recording Charges: $92Transfer Taxes: $519Your pre-paids and taxes will depend on how you set it up. 

(We'll be using the BP calculators to present this information quickly)All loans will be assumed for 1 Year at 5%APR; If the loan is pre-paid the 5% will still be due. 

Also, no points as pre-paid interest is common on private money and applicable to any equity funded note (seller financing). 

There is no way to tell without a full break down of al the fees, and prepaid insurance and taxes.