I have the same problem as mentioned in the now closed report "DVI and PDF Auto–Update does not work - ID: 3488658" (https://sourceforge.net/tracker/?func=detail&aid=3488658&group_id=192583&atid=941981)
I am generating DVI and PDF files with LaTeX, which I then view in Skim V 1.3.19 (70) on Os X V 10.6.8. I updated Skim yesterday (I guess from 1.3.18). Auto–update of DVI and PDF files is not working since.
What I did:
Delete and install latest version of Skim.
Mountain Lion, TextMate, Skim (all updated)
I also think it has to do with either Skim or TextMate + Skim. If I change the PDF viewer in TextMate to Preview or else, changes in the LaTeX document are immediately present in the PDF. When I switch back to Skim, the PDF is not updated or updated after countless attempts.