Perhaps you use a plugin that rewrites config.xml when it exits? NMTInstall will avoid this by shutting down the recording service before making the changes.
I believe the only things other than the standard install that I have running are MovieWiz and CommunitySkin. I have no problem running the NMTInstall. What do I need to do for a 2 PCH setup? Do I run it twice? Does it require the guest account?