EMM386 not installed - protected mode software already running.

More on the "Hoo Boy this is going to be interesting" front:

I've made a little progress with the previous problems, now realizing 
that the system needs to be initialized.

I have (I think) copied the files necessary for system initialization to 
a directory under ~/.dosemu and switched my dosemu.conf to point to this 
directory for boot.  I know this configuration is correct because it 
behaves differently than when it is not present - namely the system does 
not successfully load.  This directory, unlike the stock one, is set up 
for MS-DOS, not for FreeDOS.

The symptom manifests itself as an error message eventually leading to a 
non-load of the system.  Typing F8 during config.sys initialization 
shows me the following as it steps through my config.sys

BREAK=OFF[Y,N]?Y
FILES=30[Y,N]?Y
BUFFERS=30[Y,N]?Y
STACKS=9,256[Y,N]?Y
DOS=HIGH,UMB[Y,N]?Y
LASTDRIVE=V[Y,N]?Y
SHELL=c:\dos\command.com c:\dos\ /E:1024 /P[Y,N]?Y
DEVICE=C:\DOS\HIMEM.SYS[Y,N]?Y
DEVICE=C:\DOS\EMM386.EXE frame=none x=C000-C7FF x=E000-E7FF  [Y,N]?Y
EMM386 not installed - protected mode software already running.

What does this mean?  What protected mode software is already running?

Please forgive my noob questions but it's almost 20 years since I worked 
with DOS or had to think about HIMEM.SYS, EMM386.EXE and the like.

Steve Cohen