So I seem to have the same problem as the currently open bug in Eclipse 4.2 - keyboard shortcuts appear to stop working intermittently.
This has a funny workaround for those frustrated by it. Martyn Cassidy says:
I also have problems with shortcut keys after a couple of hours use. I have found that the shortcut keys are being actioned but in a tab I was previously working with, so to me it looks like the keys aren't working because they have no effect on the code I am looking at, but then if I switch back through my editor tabs I find with Ctrl-D for example the last line of code I edited in an older tab has been deleted. To get the shortcuts to action on the correct editor I have to find the tab that is taking the action and give it focus then go back to the editor I actually want to work with, and this time the shortcut keys switch with the tab and are actioned correctly.