On cart.php line 280 you have:
if (1==1 || (WA_Auth_RulePasses("Wholesaler") && $eCartNewPurple->DisplayInfo("minimumQuantity"))) {
it should just be:
if (WA_Auth_RulePasses("Wholesaler") && $eCartNewPurple->DisplayInfo("minimumQuantity")) {
That is why it is always displayed. I updated that and I added a script to the bottom of the page to make sure the GO button just closes the window and doesn't submit the form.