I have a Windows share of the format \\sharename\directory$\subdir. In PERL, when I try to read the directory, it STOPS right before the $ sign, and truncate the rest of the pathname. I also tried putting a backslash before the $ sign, and still the same issue. Any ideas how to handle this?

Thanks in advance....Which version or Perl for Windows?
Which version of Windows? Ia it a 64 bit version?
Can your try running your Perl job with no other programs using the same path names? If so, that would offer a WORKAROUND.
Are all the relevant files in one folder? If so,the full path name is not needed.
Or would you consider CRATING as small partition on your drive and moving the target folder and its contents into the new partition?

A quick 'hack' would be to use BATCH to rename some folders in the path to not have the meta-char. Then after the job reverse the naming thing back to what it was.

Sorry, I am not up to date on escapes in Perl script. You will have to SPEND some time with the manual for the version you are using.
This might help:

http://stackoverflow.com/questions/2001176/how-can-i-escape-meta-characters-when-i-interpolate-a-variable-in-perls-match-o
It seems to be like your problem. Does it?
http://www.perlmonks.org/bare/?node_id=738314