OP did transactions with a BOT lower than $1 as per indicated limitations. He probably was hoping that he would not pay transactions fees.
If you are doing that many transactions, just do larger transactions where rounding is in your favor. Why is he making thousands of really small transactions? He's probably just slowing down their system anyway.
I'm on with Bitstamp on this one.
Here's an example where I paid less than 0.5% because of rounding:
I bought 0.08774 BTC and only paid 0.047%
If you bought a gallon of milk and they split your order up into 64 ounces and rounded the price of the sales tax up each one up you would be pissed too.
Again, it is ok to do this for small single orders. It is not ok to split up a large and immediately executing order into many parts. It is ONE order. If there was not enough liquidity and part went now and part later that is different, but that is not what is happening.