The Legacy Problem
The largest problem with the non-x86 versions of Windows NT was that there wasn't much you could do with them. You installed Windows on your nice new MIPS workstation, the… played Solitaire? Most software never had native MIPS portsincluding Microsoft Office.
The machines only really sold to people who had some in-house project that needed more CPU power than Intel could provide. They were of little use to anyone else because they couldn't run any of the existing software.
Most people who use Windows don't do so because they like Windows; they do so because they want to use some Windows-only applications that they want to run. Windowsor any other OSis just there to enable this. Because most Windows applications are distributed as x86 binaries, this means that any non-x86 system is intrinsically less attractive.
This is less of a problem for open source operating systems, where most software comes in source form and is portable to different architectures, but it's a big problem for Windows.