64bit Windows versions don't support 16bit programs - this includes all DOS stuff, as well as win3.x style 16bit windows programs. This was a natural thing to drop support for, considering x86-64 doesn't support running 16bit code, and Microsoft would then have needed a CPU emulator. And not a big issue, since most people won't have a need for running that old legacy code.
However, the funny part: for whatever moronic reason, some of the various installation programs chose to write their installer stubs as 16bit code, even for programs that are meant for 32bit systems. This is a pretty braindead thing, and unfortunately does affect some programs. I'm not sure if there's any official fixes, but fortunately I haven't needed to install old software in quite a while - the programs I might have had problems with generally don't need reinstalls, and have thus survived numerous windows reinstalls (copy c:\usr\prg to another partition, move back after reinstall).