FWIW, I had what I think is a related problem and came up with a workaround: I wrote a Chrome Extension that did an document.execCommand('paste') into a textarea with focus on window unload in order to populate the element with the system clipboard contents. This worked 100% of the time manually, but the execCommand returned false almost all the time when run under Selenium.
I added a driver.refresh() after the initial driver.get( myChromeExtensionURL ), and now it works 100% of the time. This was with Selenium driver version 2.16.333243 and Chrome version 43 on Mac OS 10.9.
When I was researching the problem, I didn't see any mentions of this workaround, so I thought I'd document my discovery for those following in my Selenium/focus/execCommand('paste') footsteps.