Problems with Preconditioning for ODE Solver

I'm trying to solve a dynamic FEM Problem for a 3D cantilever beam with 2 Elements. I enterred the Input in mm, N etc. Now when I calculate rcond it gives me 3^-11. So I tried to precondition the matrix. By doing this i got an rcond of 1, which is very good. When I now solve the Problem once without and once with the preconditioning I get a result which I don't understand. Without Preconditioning it took me 400 sec to calculate the solution and with the preconditioning 932 sec?! I thought by preconditioning I can speed up my calculations because they are very slow? Do I get something wrong?