According to this site: https://bitcoinfees.earn.com/ Your fee that was actually paid is definitely not that, though I'm not sure why? Can you go to help>debug click the "console tab" and type help and try to find the command that looks like "gettxfee=<nblocks>" (I'm not entirely sure of the actual command but gettxfee=1 will output what it'll be if you want a priority transaction. You could try going town to see if you can get anywhere close to your fee however I think that'll take a while. The only thing I can think of is that several miners have tried including their transactions that have lower fees and are therefore altering the one that you set as they'd alter the average that would be gathered. Also the node you were connected to could have been configured wrong - though if you set the fee manually then this shouldn't happen.

The only thing I could suggest is to try to get someone to double-spend your transaction to get it pushed through with a higher fee if you need the transaction to go though quickly. You could try to resend the coins if that's all the money in your bitcoin wallet. If not then you might end up getting both the transactions confirming. Unless the other addresses/accounts are controlled by you in which case you can leave both going.