Sorry for the delayed response.

I use Typeset & View so the changes I made to latex_watch.pl must then be irrelevant.  Fyi, I never thought there was ever a problem with the refresh_viewer script.  I always thought that the problem was that the script was being called from elsewhere with the wrong viewer supplied as a parameter.  I could not track down where it's called from (I know very little about bundles) so my workaround was to just rewrite the script to open Skim regardless of what viewer it's given as a parameter.  I mentioned this only because it pinpoints the code that is opening TeXShop, and hence might have been helpful information for debugging the issue, though that may now be unnecessary: