cPanel X's File Manager module seems to add trailing carriage returns at the end of the PHP file (after the !>). You need to edit your PHP files some other way and upload them, or re-edit the file remove the extra lines.
Added by Carnuke: I also found this to be the case when editing my mainfile.php with cpanel. It left trailing lines after the !> and caused all kinds of problems.
Mithrandir's comment: Trailing carriage returns after the ?> will start the HTML output and cause errors if the code is subsequently trying to add/modify the header information - such as a header('location:') redirection or other header information
These carriage returns in mainfile.php can essentially result in the dreaded blank pages.