While Website Pro fully supports WordPress short-codes, it does not support PHP short-codes (<? at the top of a file). Support for these has been removed from PHP as of 7.0 as it can conflict with other types of files (such as XML).
Generally, it is recommended to use <?php instead, as this will help the system know to treat the file as PHP code. If your site currently uses PHP short-code, you can use a program (such as Notepad++) to find and replace all instances of the short-code.