Can you confirm that there is data on the zap2it website for the channels you are looking for?
Also, check the epg source in the tvheadend webUI.
Finally, take a look at the xmltv.xml file and see if the channels that are missing are in that file or not.
You are probably seeing the zap2xml epg source data as if you had that running in the past, it will still be there, unless you go to the EPG GRABBER CHANNELS tab and delete all the ones for zap2xml. (note you need to be viewing the UI in expert mode to see that tab)
Also - you can reload the epg data into kodi by going into the kodi settings/pvr-live tv settings/and selecting clear data.