I'm having the exact same issue!
Just installed VW 2012 and updated with the latest SP. Running Win 7.
I accidentally clicked the close pallet X in the title bar of the Basic tools palette. When I went to Windows>Palettes to select the Basic Tools I was unable to restore the palette by checking next to the name. The same is true for Tool Sets. I switched to a different workspace and the basic pallet appeared, when I checked the X again to see how I could restore the Basic tools in my normal workspace (Spotlight) it too disappeared and could not be re-opened. The reverse is true for the Tool Set pallet. While visible, I am unable to hide the Tool Sets by using the Window>Palettes menu. I have restarted, updated the service pack, opened and closed various documents, made copies in the Workspace editor, nothing works. Once I close the Basic and Tool Sets in any given workspace, they disappear forever.