In addition to the CSS in your Theme there are a few areas where code could be placed the would affect your Breadcrumbs (or any other piece of standard functionality).
- The Advanced Section specifically the Java Script Code section.
- The Footer which can be accessed from the Control Panel (Presentation -> Footer)
- The Header located at /admin/presentation/header
If you are having issues with the Breadcrumbs appearing and you are not able to find the reason in any of these areas feel free to submit a Support Ticket (firstname.lastname@example.org) with the details.