Chris,
Is it possible that you have installed a new application or driver since
you last used MSConfig? If so then that application is possibly either
using or accessing either autoexec.bat or config.sys when run and the
system notices this and checks when opening MSConfig for any changes that
program might have made to those files.
I have a similar problem on a Win Me box here that has an old
Ensoniq/Creative PCI128 sound card the drivers for which poll and open
autoexec.bat each time the system is booted but makes no change. The
result
is that each time one uses MSConfig one sees the environment variable
message.
Other than the message it isn't a problem and it isn't as if one is using
MSConfig all the time.

Signature
Mike Maltby MS-MVP
mike.maltby@gmail.com
> I've often done start/run/msconfig to check there is nothing odd which
> has been added to my system. I've never had to change anything,
[quoted text clipped - 14 lines]
> Thank you
> Chris
Chris Lynne - 22 Jan 2006 21:36 GMT
Thanks for your reply Mike. I honestly haven't installed (or even
re-installed!) any new hardware or software for - I can't remember how
long! - which is why I suspected virus/spyware/whatever. However, as
you say the message isn't a problem, that's good enough for me, and
I'll live with it!
Thanks again
Chris
Noel Paton - 23 Jan 2006 09:41 GMT
You may find that opening autoexec.bat and config.sys in Notepad will give a
clue as to what setting is being adjusted - if you need a second opinion,
post the contents (NOT the files!) here, and either Mike or myself will be
happy to look at them (or anyone else, for that matter!).

Signature
Noel Paton (MS-MVP 2002-2006, Windows)
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Please read http://dts-l.org/goodpost.htm on how to post messages to NG's
> Thanks for your reply Mike. I honestly haven't installed (or even
> re-installed!) any new hardware or software for - I can't remember how
[quoted text clipped - 4 lines]
> Thanks again
> Chris