I'm having a few issues using the non-default workspace in Flash Builder (beta 2).
1. Not seeing files in a workspace
a) Create a new directory on desktop to use as a workspace
b) Switch to that directory in Flash Builder and create a new project.
c) Later on, I add new projects to that directory. As an example, say I just drag the Flex 4 training projects into it.
d) Reload directory in Flash Builder and I will still only see the project that I created in Flash Builder. Not the training projects.
2. Different behavior in non-default workspace
a) Create a new directory on desktop
b) Drag training files into that directory
c) Launch Flash Builder and switch to new workspace. All training projects show in the Package Explorer
d) Edit code in a project MXML file to cause an error and save file.
e) Error will show in the Outline panel, but not in Problems. Also, there is no red error box next to the file name.
Based on your steps, this is expected.
In scenario #1, you've created a workspace, opened the workspace in FB, then performed a file system copy. Eclipse is still not aware of the projects. You'll have to import the projects into Eclipse under File > Import > Existing Project into Workspace.
For scenario #2, you're creating the workspace on disk before Eclipse knows about it. When launching into a "brand new" workspace (at least, it's new to your Eclipse installation) it will look for existing projects automatically. That explains why the projects show up in Package Explorer in this scenario.
What isn't explained yet is the lack of errors. Perhaps the projects you're working have .actionScriptProperties file settings that are invalid? Missing path, invalid SDK, etc.?
Jason San Jose
Quality Engineer, Flash Builder