There is a utility included in WinPE that can be found under x:\ldclient called fixwindows.exe. It will rearrnage your drive letters so that the c drive will actually be the right partition.
If you add a execute file action for this exe before any script injections then this should solve your issue.
That must be it! We haven't had any of those failures since I added it.
Sorry for the late reply and points, but I wanted to give it some time before I counted it resolved.
I use the Micrsoft DevCon utility in my task sequence prior to any DiskPart commands
I use it twice: Firstly to disable any USB-based card-readers that may have picked up drive letters:
Devcon.exe -disable "USBSTOR\GenDisk"
And secondly to disable any CD/DVD/BD Drives:
Devcon.exe -disable "*GENCDROM*"