I just found the answer (to disabling the designer anyway): http://blog.flexicious.com/post/Flash-Builder-Burrito-Problems-View-Stealing-Focus.aspx
To quote from the post: "Although we were unable to find a way to resolve these errors, we could make them go away by disabling the design view altogether. You can do this by going into Window-> Enable Design View."
I just did this and the problem is now solved!
(However, I'm leaving this question open in case someone from Adobe knows how to solve this without having to disable the designer)
These issues will be resolved in FB 4.5 .
These issues *should* be resolved in Flash Builder 4.5, but they still seem to persist for me