I am not being facetious with my answer but have you considered simply using XCode and Apache Ant and creating your own build script? This is the approach that I've had the fewest of problems with. The reason being is that Ant is Ant no matter where it is. It also cuts out all the background noise (i.e. configuration files, scripts, etc).
I have had similar problems like what you've mentioned using Netbeans and Eclipse (e.g. a version change or an SDK change and suddenly my project is somehow foobar).
As for your error message:
"An unknown item is declared as the root of your MXML document.Switch to source mode to correct it."
StackOverflow seemed to have a solution:
Don't know if it's your solution. Sometimes these automated tools place little hidden scripts in their comments that are meant to mean something for the drag-and-drop GUI editor and deleting these comments confuses the IDE.
I am not familiar yet with either Ant or XCode. I invested into Flex Builder, I'd like for it to work for 100% of what I need. I'll check into those tools though.
Update... Since I'm back in my office I downloaded and reinstalled SDK 3.3 on my MacBook. Same problem still happens every time I try to go to Design mode in the main app or any component: "This component is based on ______, which is not a visual component. Switch to source mode to edit it"
If anyone can point me to a solution to the design mode failure, I'd sure appreciate it.
I found a posting at http://thoughts.novaleaf.com/johanm/2009/05/25/solution-error-this-component-is-based-on-a pplication-which-is-not-a-visual-component-switch-to-source-mode-to-edit-it-flex-builder/
that indicated Flex Builder 3.0.2 is required to be able to design with SDK 3.3. I downloaded and installed 3.0.2 and my design mode is working again.
Now I am still trying to figure out why it can't create a Flex Project Archive...