when you say "whenever I try to root it"
i dont understand what you mean.
should be a one time process.
Also, I noticed in SuperOneClick if you click "root" instead of "shell root" and manually push busybox over, then it causes some WEIRD things to happen. I learned from that mistake.
you should be able to shell root, push busybox and su over, make them rw, then reboot, have a permanant root, and nothings affected.
what is the method YOU are trying to use