All of our giveaway's entries are based off the subtotal of your order. So in short, yes, discount code will unfortunately affect your entries. As your subtotal goes down your entries will also go down, just like your entries going up with your subtotal!
Unfortunately, we don't have any current work arounds for this, as it's embedded in our official rules and something we have to abide by.
Do make sure to check out the information on our bonus entry codes, so that you can get extra entries at no extra cost!