Cygwin 1.5.5 Configuration problem

["Hughes, Bill" <Bill dot Hughes at cox dot co dot uk>]

I have tried rtfm, rtffaq, rtfa(rchive), I would appreciate some help if
someone could point me in the right direction.
I was having problems with man (among other things) not working so I decided
to perform a complete uninstall and re-install.
I un-installed everything, removed the remaining folder tree and deleted the
cygwin entries from the registry (after exporting).
I then downloaded almost everything to a local directory, rebooted the pc
and ran setup again to install everything I had downloaded to D:\cygwin.
I set the HOME environment variable in 2000 to D:\cygwin\home\hughesb, in
cygwin this is set to /cygdrive/d/cygwin/home/hughesb

When cygwin was started the pwd was /cygdrive/d/usr/bin, not /home/hughesb,
'cd #' then moved pwd to /cygdrive/d/cygwin/home/hughesb (not
/home/hughesb).
I got around this by creating a .profile with 'cd #' in it, which does not
seem ideal.
I then set CYGWIN to 'check_case:strict ntea ntsec title', which I used to
have.

I'm not sure if it's relevant but I also did the following:
mkpasswd -cl > /etc/passwd
mkgroup -l > /etc/group
mkgroup -d domain >> /etc/group
to get NT security working, I edited the relevant entry in /etc/passwd to
refer to my home directory. 
HughesB:unused_by_nt/2000/xp:15439:10513:HughesB,U-COX\HughesB,S-1-5-21-4511
12558-379081443-316617838-5439:/home/hughesb:/bin/bash
and removed the 'cd #' from .profile, but this left me at
/cygdrive/d/cygwin/bin.
I also set USER to HughesB in 2000.
I can't find anywhere that I can effect from /cygdrive/d/cygwin to / - what
have I missed, please?
I am assuming this is a problem with what I have done/not done and not a
bug.
btw man is still not working but I've deferred that until I hopefully get
somewhere with this problem.

Output of cygcheck -svr attached.

regards,
Bill Hughes

 <<cygcheck.out>>

Attachment: cygcheck.out
Description: Binary data

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