Yes, it is designed to work under WinPE. No idea yet, at least an error message should be displayed, if there is any problem with bootmgr or Boot\*.* files creation. actually not, bootmgr should be created on the partition you selected. It's difficult to say, which disk is the "wanted" boot disk as the program is mostly use from WinPE or Portable Windows.Also as you noticed Windows detects different between IDE, SATA, USB, ... I'll try to improve it.