I'm using a Radeon HD5850, so it isn't exactly the same card, but your experiences should be similar.
In older versions of Ubuntu, the open drivers were not very good and you almost had to use the proprietary drivers. In 11.04, there were great improvements to the open drivers, but there were still a few issues with Unity, although they were minor. In 11.10, there is no doubt that I prefer the open drivers. They're faster, more stable and makes things easier in general.
In other words, unless you have very good reasons not to, I would strongly encourage you to check out the newest versions of Ubuntu and see if the problems just go away.