[janbar]

Yes. If you switch off "using backend number", all of the channels are shown in the epg screen.

So as nickr said, the root cause is backend channel number are not as integer number. Here they contain alpha-numeric characters breaking the cast to the XBMC channel number.
Since Helix the subChannel number exists and could be help to resolve this case. But now for Gotham the only way is to miss the separator "_" or "." assuming all channels use ATSC number. If not we will have always conflict between ATSC channel (2_1) and others (21).

I pushed a commit to concat major and minor parts for Gotham: 2_1 => 21 or 2.3 => 23
I pushed a commit to transfer sub channel number for Helix: 2_1 => 2.1 or 2.3 => 2.3