I think you might be talking about a Byte-order mark - which is something that can be silently added to template/ini files, etc. if you use certain Microsoft text editors to edit those files.
Which means that you would see a three-character garbage string "" come out and that's it. Is that what you are talking about?
If it is:
Do a search for BOM in the forums and take a look at this: http://ez.no/developer/forum/setup_design/strange_characters_generated_by_ezpublish
I have a shell script that might help in finding the files with a BOM in:
