An installation of DOS (e.g. MS-DOS 5.0) will typically include a statement in its CONFIG.SYS such as
When installing Windows 3.1, it's setup comments (REMs) that line out, and adds
Presumably there is some material difference between these two files for the setup to make this modification. What does the Windows version do that the DOS one doesn't?
(This question is prompted in part by an Aleph One expansion card for Acorn Archimedes machines, which adds hardware support for running PC software under RISC-OS. Loading the DOS version of HIMEM.SYS results in an unstable system, but the Windows version works correctly, even when running DOS. A forum discussion about these symptoms can be found here.)