I have the exact same (frustrating) problem with Ubuntu 14.04, XFCE and the latest version of Sublime Text 2.
I tried every mentioned solution: disabling ClipMan, copy_with_empty_selection: false etc..
The only one that seems to work is disabling the Xfce Settings Daemon, but doing so makes the OS quite unusable (most icons dissappear for example).
Is the problem solved with ST3?
Any help would be much appreciated!