Btw. the line Options Indexes FollowSymLinks +ExecCGI is not valid syntax. Option lines without any +- set the options while option lines with all +- merge them with the options of outer sections.

See "Options" in the apache documentation.

EDIT: Oh, didn't realize: That could also be the reason why +ExecCGI doesn't work for you. You would have to change all the option lines in the other directories to use + and -, so that they don't overwrite your setting of ExecGCI in the root. And in the root the '+' in "+ExecCGI" should be removed.

Changing the option lines to +- changes their logic. So instead of reworking every options line it might be easier to just add an 'ExecCGI' after all.