What version of emc are you using? Have you updated to the latest? If you just installed the livecd and not updated it you are running 2.4.3. there have been a lot of fixes since then. If you look here
LinuxCNC Documentation Wiki: Released
You can see that 2.4.5 relaase had some fixes (and past that there are a lot more)
pncconf: fix inverted encoder
pncconf: fix following error when inverting servo direction
Maybe that is your issue? I have not used the pncconf.. You really also should get comfortable editing the hal and ini files also. The pncconf though will give you a good starting point.
sam