I encountered a mystery surrounding several missing menu options in one of my Flash Builder workspaces recently. I wanted to create a new skin for a List control so I right-clicked on my skins folder and looked for the New MXML Skin option. And I looked. And I looked some more. But it wasn't there.
I happened to have another copy of Flash Builder open in another workspace so I gave it a try in that project. Sure enough, the New MXML Skin option was there along with a couple of other options that were missing in the first workspace. Here's a list of the menu options missing from the File --> New menu in this workspace:
I'm not sure why those menu options went missing but I was able to work around it by recreating the workspace. I simply created a new workspace, copied all of the projects into the new workspace folder and then imported all of my projects into the new folder. I then had a full set of menu items.
I poked around a bit trying to figure out what went wrong but wasn't able to find a conclusive answer. My best guess is that it has something to do with the fact that I was previously running the Flex 4 beta and that's when I created the workspace with the problem. I compared the workspace .metadata folder and, curiously, there were 25 folders inside the .plugins folder for the problem workspace but only 12 for the newly created one.
This is an eclipse thingy, menus get cached in the workspace' metadata. If you try using a newer build of Flash Builder with a workspace from the previous version, you may notice this behavior.
The workaround is to create a new workspace and import all projects there.
You can also try window -> reset perspective.