I have experienced some problem related with tags in Alfresco Sites in Alfresco 4.1.1 EE and Alfresco 4.2.c CE (only in Sites, there is no problem with the repository). In some moment (this is a problem because I can not reproduce it, only that there is a problem), the tags are not synced and you can't see them in the Tags Browser or even in Tags cloud component.
The way of solving them works for me, and i created a demand action in Tags cloud component for rebuilding tags in Site, but it is a workaround forcing the sync process via JS API.