I don't really know how to describe this, so I made a video:

http://ge.tt/4lG2iMS1/v/0

You can see me start a deadlink scan (of www.lfrz.at) and then observe the following:

second 12 - I switch away from deadlink and try to open the assets app while the scan is running. Note how the app opens, and then everything locks up. I can't get back to admin-central.

second 35 - I started the scan again, and now I switch around, I can switch to the assets app (which is already open), but when I start the pages app things become locked again.

second 70 - I started the scan a third time, and switch around between the apps. Note the very cool effect that happens after about second 75 - the UI begins to switch between the pages and deadlinks apps all by itself, back and forth. The animation effects when swirching apps make it look kind of smooth and cool, but I don't think it's desired behaviour

It's not browser-specific. I recorded this video on firefox, but I got the same thing to happen in chrome...

At a guess: maybe you're calling something UI-related from the worker threads? (not allowed, Vaadin is not useable by multiple threads concurrently!)

Or maybe the problem is more that the original command runs for too long...
The threading is realized in a pretty weird way:
the ScanCommand loops over the pages to scan - but this happens within the UI thread. Each page to be scanned is loaded and then the Links are scanned. Then the links are all checked, and only the link-checking happens in the worker-threads.
IMHO this is not the right approach. The entire scan, ie already the loop in the ScanCommand should be handled by the worker threads. The ScanCommand should return control to the UI thread immediately.