ISE 10.1 does not reload the user constraints file

Hei,

I have to use ISE 10.1 because I have a spartan2 design (must be 5V 
tolerant).
If I create a new project and add a user constraints file with some 
pins, and then I delete some pins (not yet used) the mapper complains 
that the pins I deleted from the ucf are unconnected. As if the pins 
were still there.

Choosing clean all project files and re-run all does not solve the 
problem...

Any ideas ?

ps: I am planning on using the command line tools if I can avoid this 
problem.

Any tips are welcome.