The default “Setup Windows and ConfigMgr” SCCM action will effectively replace all variables in sysprep.inf
And since that action is run under WinPE, the %WINDIR% variable will be replaced with X:\Windows.
So never, ever use that variable in sysprep.inf… (unless you really deploy Windows to X: which I highly doubt 🙂 )
This is by design….
It’s not only WINDIR…