One of things we are seeing come up regularly is that in regional areas there are commonly a couple of channels that have the same LCN, while normally this is not a problem Plex will ignore any channels with a duplicate LCN.
The good news is there an easy fix for this, on the Guide Settings tab in the My Account menu on the IceTV website you can modify the list of channels that is downloaded by Plex, or limit which LCN's are sent for each channel, if you change these settings and click on Save then just refresh the guide within Plex you should see the updated channel list immediately.