As we know if we have a lot of fields and a lot of roles the number of workflow_fields checkboxes rockets. In the current project I'm on we have a workflow_fields page with nearly 4000 checkboxes.

PHP has a setting "max_input_vars" which you may need to adjust (we did, after tearing our hair out for a couple of hours). You can't set it with php_ini(), has to be in php.ini or httpd.

Also, depending on the PHP you have installed: "suhosin.post.max_vars" and "suhosin.request.max_vars"