So....she was able to pick up her passport at the visa office but only after some very confusing steps.
First, she went to the visa office since the ePay site wasn't working and thus DHL pick up would not work. (Apparently there are two pick up options, DHL or the visa center) but the visa center said because you selected DHL on the application, they can't do anything. You need to email the US Embassy and explain that you want to switch to the visa center pick up.
So she emailed the embassy and about 30 minutes later, she went back to the visa pick up office and got her passport. It also cost nothing to do this option, if you are staying in KZ for a week or so there is no reason to select the DHL option.
Hope this helps. We never got the ePay to work so not sure what the issue was.