Have you checked in the Event Viewer to see what the actual fault is?
Usually with FTM it reports a problem with the .Net framework.
If it is a.Net problem then in the past I've removed the .Net installation and then done a re-installation of FTM.
If you do need to remove a particular .Net installation then there is a tool available which is pretty thorough.
http://blogs.msdn.com/b/astebner/archive/2008/08/28/8904493....
I've used it many times in cleaning up errors.
Usually with FTM it reports a problem with the .Net framework.
If it is a.Net problem then in the past I've removed the .Net installation and then done a re-installation of FTM.
If you do need to remove a particular .Net installation then there is a tool available which is pretty thorough.
http://blogs.msdn.com/b/astebner/archive/2008/08/28/8904493....
I've used it many times in cleaning up errors.