There's so little to this that hopefully there's another explaination but I'm seeing one. I had 0.30239966 bitcoins and I tried to send 0.3 to someone. It warned me that because it was over a size limit, it was going to charge 0.005 so I accepted and now I have 0.00 as a wallet balance but the transaction went through. That means it only paid .00239966 as a fee. That's not 0.005 so that's not supposed to happen right?
I have had this happen to me also, the fee was much higher than the normal 0.005 and it took the remainder of my bitcoins as the fee