php and html tag problem when customizing menu items
You could check if where the call to the l() function is created (in the function mentioned: bootstrap_menu_link), the third parameter contains the following element in the array:

'html' =&gt; TRUE


This tells drupal to output the title of the link as html and not run it trough check_plain().

Also, I would create a custom theme based on the bootstrap theme and add my customization there.