Every 5 minutes my Flash Builder 4.6 install hangs for 20 seconds. I had the same problem with version 4.5. BTW the download page said to uninstall 4.5 and then install 4.6 and all my project settings would be saved. This was untrue and wasted a lot of time getting everything back in order.
I also use Flash Professional 6 at the same time as Flash Builder.