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I don't use swaret I use slapt-get but I hear that they are similar.
I once had an issue where I had done --upgrade and then my Gnome wasn't working correctly.
I found out from posts on here that you sometimes need to be checking the changelog for the packages when they are updated. That is, sometimes there are packages added and/or removed...slapt-get and swaret (AFAIK) do not deal with this...they merely look at what you've got and look for newer versions of what you've got.
Once I looked at the changelog and manually added necessary packages and removed those that were removed my Gnome was working again happily.
The only time this happened to me was when Gnome was upgraded by a big version step (hasn't been too long ago). The other hundreds of times I use slapt-get I have not had this issue, just that one time.
Maybe my thoughts have nothing to do with your problem, but maybe help in the future.