As far as I can tell, it is triggered when skim reloads a changed PDF file, but I haven't been able to completely reliably find out exactly what triggers it. At first I thought it was to do with the pdfsync functionality, but then I noticed it could be triggered simply if the files changed.
Aside of whether this is a Skim bug or not, IMHO it is recommended to switch OFF checking for file changes in Skim Sync properties while you're using Latex bundle, which anyway forces Skim to reload the file upon each compilation.
Regards,