The path should probably be /cygdrive/c/cygwin/home/Administrator/test.chr if the OP's Cygwin installation is anything like mine.

Now that I'm home, with a box that runs cygwin:
Windows cmd shell

C:\cygwin\home\Keszler>dir
 Directory of C:\cygwin\home\Keszler
12/08/2011  07:33 PM                12 test.chr
12/08/2011  07:35 PM    <DIR>          x

C:\cygwin\home\Keszler>cd x

C:\cygwin\home\Keszler\x>dir
 Directory of C:\cygwin\home\Keszler\x
12/08/2011  07:35 PM               155 test.pl

C:\cygwin\home\Keszler\x>type test.pl
#!/usr/bin/perl
use strict;
use POSIX;
use warnings;
open (NEWFILE, "/home/Keszler/test.chr");
print "Start";
while(<NEWFILE>)
{
print $_;
}
print "end";

C:\cygwin\home\Keszler\x>test.pl
readline() on closed filehandle NEWFILE at C:\cygwin\home\Keszler\x\te
+st.pl line 7.
Startend
C:\cygwin\home\Keszler\x>
[download]

cygwin shell

$ pwd
/home/Keszler/x

$ ls -l
total 1
-rwxr-xr-x 1 Keszler None 155 Dec  8 19:35 test.pl

$ ls -l ..
total 1
-rw-r--r--  1 Keszler None 12 Dec  8 19:33 test.chr
drwxr-xr-x+ 1 Keszler None  0 Dec  8 19:35 x

$ cat test.pl
#!/usr/bin/perl
use strict;
use POSIX;
use warnings;
open (NEWFILE, "/home/Keszler/test.chr");
print "Start";
while(<NEWFILE>)
{
print $_;
}
print "end";

$ ./test.pl
Start1,2,3
a,b,c
end
$
[download]