I looks like the checking to ensure that a new building is connected to the existing buildings in a base has a bug when it comes to the buildings that require 2 tiles - such as the workshop. This can easily be recreated in a new game by deleting and trying to rebuild the alien containment facility. It does appear to work if both parts of the building are next to existing buildings...
I'm running ufoai-2.4-dev-1295896845-Debug-full-win32 on a intel i3 if it makes any difference...