Are we still talking about the VA IRRRL loan?
Two things:
1- If you had a 60 day lock on 4/28/09, that would leave you until 6/27/2009 to FUND the loan. 6/27 was a Saturday, so you really would have needed to fund by Friday, 6/26/09. With a 3 day right of rescission, that means you would have had to close by 6/22/09, which is the date of your post. So, I think that information is spot on.
2- On VA loans, the types and amounts of fees are pretty strictly controlled. Basically, you can have government fees, title insurance, appraisal, credit report, and 1% of lender/broker charges. To maintain compliance, many lenders will always list all their normal fees, even if they have to discount them. Or, in the case of a brokered loan, the lender will charge the fee, and the broker will then pay it.
Without seeing the HUD/GFE, I can't say for sure, but I can say that it's not uncommon, particularly with VA loans, to see fees charged and also credited.
westy is correct though. The main thing to pay attention to whether or not the deal makes sense for the cost.