Hello,
Thanks for the report : it's a bug.
Colors with stereotypes have been implemented lately in the code, so sometimes it's not taken into account. Fortunately, the correction is usually very easy.
So you can find here a beta
https://dl.dropboxusercontent.com/u/13064071/plantuml.jar that fixes this bug.
This will be included in next official release.
Thanks again for the report : it really helps!