Up until recently, I almost never kept more than one project open in Flex Builder at the same time. The reason was simple: if I was looking at Project A, I found it very confusing to see bookmarks or warnings from other projects in the Bookmarks or Problems panel.
Several months ago, I looked for a way to filter this, but for some reason I couldn't find it. Last week, I was more successful. If you click on the filter button () in either the Problems panel or the Bookmarks panel, it will take you to a dialogue where you can select an option that more suits your working style. I selected "On any element in selected project."
Now I can have multiple projects open at once without getting distracted.