Bootstrap is a great Drupal theme that makes it so your form elements and other Drupal things get output with proper Twitter Bootstrap CSS attributes. One downside to it is that the popular Webform module has elements that don't get styled by the Bootstrap Drupal theme and then they look like unstyled form fields.
To fix it, go to Bootstrap's theme/process.inc file. Inside it, add 'webform_email' to the 'types' array in the _bootstrap_process_input() function. This will style Webform's special email field. Other fields likely have different types. The reason it doesn't get styled is because the 'types' array is coded to look for only default types and not the special ones that Webform is using.
If you want to see what the #type is on an element, I recommend installing the Devel module and calling "dpm($element);" inside the theme/alter.inc bootstrap_element_info_alter() function. This will output all of the elements on your current Webform.