Here is my old "MSDOS.Sys" file. It is configured to DISABLE load of Win.Com. Deleting (back it up first) the [Options] parameters listed in your MsDOS.Sys file should restore DOS to the default of loading Windows on boot.
Ignore what was mentioned before about the "DOS" parameter having to be set to "Auto". That I believe is only relevant for Win98 and not Win95. The easiest way is to do what was mentioned previously... just add "Win" to the end of your "AutoExec.Bat" file using the "Edit.Com" program.:
MsDOS.SysQuote
[Paths]
WinDir=C:\WINDOWS
WinBootDir=C:\WINDOWS
HostWinBootDrv=C
[Options]
BootMulti=0
BootGUI=0
WinVer=4.10.1998
BootKeys=1
;Changes added by me 6/30/98
Network=0
BootWin=1
BootMenu=1
BootMenuDefault=1
BootMenuDelay=1
BootDelay=0
BootConfig=1
BootSafe=0
Logo=1
DisableLog=1
LoadTop=1
SystemReg=0
;End Changes added by me 6/30/98
;Begin Changes added by me 10/28/00
DoubleBuffer=0
AutoScan=2
BootWarn=1
DblSpace=0
DrvSpace=0
;End Changes added by me 10/28/00
;
;The following lines are required for compatibility with other programs.
;Do not remove them (MSDOS.SYS needs to be >1024 bytes).
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxa
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxb
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxc
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxd
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxe
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxf
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxg
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxh
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxi
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxj
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxk
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxl
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxm
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxn
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxo
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxp
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxq
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxr
;xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxs