There's nothing magic about '.' files as far as tar is concerned. Without a more complete sample of what you're doing beyond just the tar command used:

• setting of variables used by command
• error-checking code
• whether you do anything with the tarfile after you create it
• ...

it's hard to suggest what's wrong. About the only thing that would prevent tar from including files would be permissions. The single snippet you provide doesn't indicate that you're checking the output of the tar command, which would write things like "tar: dir/.please_include_me: Couldn't visit directory: Permission denied" to stderr if the user the script is running as didn't have permission to read the file. Without seeing the code, I would suggest adding the -v option to the command in your script and capturing all of stdout/stderr. It might tell you something

fnord