Yesterday I want to create a Boot media with Windows 7 USB/DVD Download Tool. This Boot media came from ConfigMgr 2012 R2, which is based on Windows PE 5 (Windows 8.1). Everything seems fine, but creating the Boot media was getting stuck on 98%. Created the Boot media a few times again, but without any luck. Finally found a nice blogpost with more information about this issue.
This post explains why the Windows 7 USB/DVD Download Tool (WUDT) is unable to copy the install files to the USB drive in some cases. It mentions: If you have problems Windows 7 USB/DVD Download Tool you can try the free alternative Rufus. Rufus is a small utility that helps format and create bootable USB flash drives, such as USB keys/pendrives, memory sticks, etc.
After using Rufus everything went fine, and USB Boot media was finally working. Hope it helps!