What version of ArtRage are you using? Also, do you know what the current display resolution is for your Cintiq? The native resolution of the Cintiq is a lot higher than the minimum required by ArtRage, but it's possible that if you have your resolution set very low that the window may be getting cut off. Is it the entire bottom part of the ArtRage window that you are losing? Also, what version of OS X are you using? Once I know a little more I should be able to advise.
Resident Bug-Hunter and Support Guy