Hello Den,
If you haven't already, I would give UCSF a call. Did you get anything in the mail from UCSF regarding your application status? Before my application was complete, they mailed me 2 letters regarding my incomplete application. Once they received my DAT scores, another letter was sent to confirm my complete application. And yes, UCSF Webtools said my application was complete. I didn't notice any delay in the processing of my application by UCSF versus other dental schools. So again, do call. Perhaps something got lost in the mail? Webtools has a checklist of what they already have from you. Just mail them whatever they have left "unchecked."
Hope this helps!