It's possible that the step where you "worked with sd4tvh addon and looked at the selected and deselected channels not changing anything" did make a difference.
It seems that the filter.cfg file is written or re-written (I checked the timestamps) when entering the "Add & Remove Channels from Lineup" option. Depending on the settings this might make the difference between sd4tvh working or not.
I think I always go into this last sd4tvh menu option. More testing is needed to see if this step is always required (at least with the current code in 0.3.4).