I would give geocators Auto Cookie Mod a try first, that will probably fix your problem. That's the only thing that I could really think of that could cause a problem. Did any one of your modifications edit login.php?
Do you have a link that we can look at?, Also, Could you provide the domain and forum path(you can get this information through a database administration tool like phpMyAdmin, in the phpbb_config table).
Look in the language/lang_english/email directory, and edit the appropriate email.tpl file, which in this case is user_welcome.tpl or if you want to edit the email with the activation link edit user_welcome_inactive.tpl