I have just worked out why I have observed confusing behaviour with subclipse. I am playing with Jeremy's new web site layout in the sandbox so wanted to update to his latest files.
I have the tuscany project checked out in my workspace so I navigated to sandbox/site, right clicked to team/synchronize with repository This poped up the team synchronize view with something like the following tree view on the left hand side tuscany sandbox/site sandbox/site/site-author some files sandbox/site/site-deploy some more files I wanted all this stuff so I clicked at the top level and selected update. What this appears to do is update to whole of the tuscany project not just the subset of files shown to be different in the synchronize view. This leads to a VERY long update which invariably fails. As it fails for me so often before it actually starts downloading anything this took me a few goes to work out what was going on. What I have to do is select each directory in this view and ask it to be updated individually. I have a slightly old version so I'm going to upgrade to see if that changes the behaviour.