I was told that SCCM and or WDS has a similar function behind the scenes to rearrange the drive letters. I use fixwindows all the time as till now was very reliable.
Just had an interesting failure where the restore of the image mounted the system restore volume as C so then both the mount and fixwindows actions couldn't run and HII failed as there was no windows structure on C for it to work with.
If it is not imagew version thanks George for testing as this was on my list (also makes sense as it has been out for a long time with no known issues) then it must be something in WinPE 4 causing the issue. Will have to do some more testing and digging if it is going to give these inconsistent results