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auctex can only see .tex files in HOME directory

I recently updated my Cygwin distribution and now aucTeX will only
work on documents (i.e. .tex files) in my HOME directory.  If I use
LaTeX from the Cygwin shell then things work fine, as they did before I
installed the updated distribution.  (I.e. I can LaTeX files in their local

I know very little about emacs-lisp, but I have identified the lines

(list "LaTeX" "%l '\\nonstopmode\\input{%t}'"
      'TeX-run-LaTeX nil t) 

in my tex-site.el file as the lines that auctex uses to run the latex
command from within emacs.  In the good old days, %t would expand to
(path to local directory)/filename.tex.  Now it just expands to
filename.tex, without the path.  

Does anyone have any idea 
1) what setup.exe could have changed to make auctex stop working
2) What I have to do to make auctex and cygwin play nice together again?

My data:
Computer:  sony vaio laptop, PIII
OS:        Windows 2000 Service Pack 2.
Auctex:    auctex-10.0g
LaTeX:     MikTeX 2.1
Emacs:     20.7.1
Cygwin:    1.3.9 + all the stuff that cygwin setup.exe distributed 
           on January 31 2002.
Previous Cygwin distribution (when everything worked fine)
      :    whatever setup.exe distributed August 2001.
astrological sign:  capricorn
The error message I get in auctex:

Running `LaTeX' on `testfile' with ``latex
This is TeX, Version 3.14159 (MiKTeX 2.1)
LaTeX2e <2000/06/01>
Babel <v3.7h> and hyphenation patterns for english, french, german, ngerman,
mylang, nohyphenation, loaded.

! LaTeX Error: File `testfile.tex' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: tex)

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