wpautop filter interfering with theme

I have a theme which is inserting <p> and
all over the place. This is causing a plugin (Event Manager) to not function correctly, as the injected tags are interfering with the DOM traversel.

I have tried adding

remove_filter( 'the_content', 'wpautop' );
remove_filter( 'the_excerpt', 'wpautop' );

to the functions.php, but to no avail. I am using a short code [event-form] to add a form to submit an event, but the validation fails, because of the JS not working correctly.

If I use the Twenty-Eleven theme, the plugin works fine, so it has to be my theme.

Has anyone had any experience with this for a custom theme before?

Let me know if more information is needed.

Thanks.