4 ways to approach it (maybe more, if i noodle on it)

1. change bbcode.inc.php to parse it properly into html that works, then content rebuild all posts
2. modify the content rebuilder to change the original (POST_DEFAULT_BODY), then rebuild it
3. hijaack smarty output to change it on the fly right before rendering
4. if there are a small number of colors used, then use 'Active Text' (control panel option) replace to make it 'right'

either way, you'll have to rebuild, so i might lean towards #2 if there is no consistent color pattern used..

or #4 if it's just a few cases..