Developing the same source with more than one person isn't fun: Everybody has his or her own style and with Perl's TMTOWTDI these style may be very different. Perltidy reformats your source to one, common style but this could be very hard when using a versioning system like SVN or GIT.
Problems start when one person forgot to tidy up the code before committing: Then next tidy'ed commit will introduce many "changed" lines where the change is nothing more than perltidy's reformatting of the previous commit. Perltidy easily introduces much more reformatted lines than the really changed lines.
You should start enforcing the tidy rules: Add a simple precommit hook to your SVN server which grabs each committed file, runs perltidy over it and compares the result to the committed file. Finally deny the commit if the two files differ - the committed file wasn't tidy'ed regarding your rules.
Perltidy on Windows defaults to Windows line endings (\r\n) instead of unix line endings (\n), force it to unix style or every single line of each file will "change" during tiding - even if your editor respects the unix format.
If anybody knows a solution, how to tidy each file within a server commit hook, please add a comment. It isn't possible to modify the file-being-committed during the commit - as far as I know.