Guillaume, the only time stereotypes have guids is when they are directly in the model instead of a profile. In this scenario there are no tagged values associated with the stereotype, so synchronization couldn't do anything.
As Paolo suggested, the t_xref table will reference a guid if the stereotype has been defined using the stereotypes list for the model.
For any stereotypes defined in a profile, the t_xref table will contain an FQName, which allows you to identify which profile the stereotype comes from.
If you are writing a script to convert between two stereotypes, you will need to update t_xref and t_object (or whichever type of element you are updating.) If they ever get out of synch EA will try to find the stereotype in t_object and save it to t_xref, creating a stereotype if none matches.
Paolo, it sounds like EA is deciding that the t_object and t_xref stereotype definitions are out of synch. It could be creating a new t_stereotypes record because it doesn't think that the stereotype can be applied to the element so no match is found.
You may also find it worthwhile to go into the user/group permissions and disable 'Configure Stereotypes' for all users. (Potentially leaving your admin users until cleaning up the rogue entries)
Qwerty, claiming a "fact" in presence of evidence to the contrary doesn't make you look good. Yes, t_object, t_attribute etc do not reference a stereotype by guid, but stereotypes can and often do have guids.