OK, can you be a little more specific about the failure mode? Does the ⌘R command terminate or just spin forever? Sometimes when Skim.app updates, Textmate will tell it to open a pdf after you compile, but the operating system will show that dialog which says “Skim.app is an application downloaded from the internet, are you sure you want to run it?”. But this dialog comes up in the background and skim seems to hang, and the document never appears.
I have been experiencing the same problem. The ⌘R command doesn't terminate it just spins forever, apparently at the point where it is calling Skim. On my system this only happens if Skim is not already launched. It works fine if Skim is already open.