won't load .emacs init file

[paul . d . mead]

I'm running emacs under cygwin. For some reason my .emacs file is
being ignored.

The environment variable for HOME is reporting correctly as /home/
paul. That is where I have placed my .emacs file. I have tried running
using --debug-init and it reports no errors.

I have evaluated every line in the file in turn and they all work
fine. It is as if it's running emacs -q, but there are NO aliases set
or scripts which could be running instead.

Close to my wits' end. Can you help?

Thanks