If the magnet covering is damaged, that might be causing your problem. Just depends on how damaged it is, sort of, and if there is other damage associated with it. That covering acts like the separation between the plates of a capacitor (magnet/car roof/metal). Changing it's thickness can and will change the effective 'capacitance' and so change how the antenna is tuned. Keeping as near to the original thickness is a good idea.
While that may be a problem, I have a feeling that it isn't the (only) cause of the problem you are having. No idea what the problem may be so can't say anything specific. I'd recommend a good 'general' look at things, no preconceptions going in, and see what you can find that's 'different'. Not a real good answer, huh?
- 'Doc