Running 6.08.00RC8 and created a folder in the data/homebrew folder to hold my additions.  I'm loading the srd5 dataset and my homebrew.  Currently in my .pcc I only have calls for DEITY:klassen_deities.lst and LANGUAGE:klassen_languages.lst in order to add a god and a language.

When I start a new character, I can see the new deity I created (albeit, on the deity list under the Domains tab, none of the descriptive text shows up), but if I try to add a language, my new language does not appear.  I'm not sure what I'm doing wrong.

Would help to show what you've got in those two associated files too.
Languages.lst needs a TYPE:Spoken.Written tag.
Dieties.lst, your text needs to be in a DESC: tag.

Thank you!  Yes, I was wondering just how much I should put into the message...

klassen_deities.lst
Muamman Duathal            SORTKEY:03_Nonhuman Deities    KEY:Muamman                DESC:Wanderers, Mace over Leather Boot                                            FACT:Title|Muamman Duathal, dwarf god of wanderers                    FACTSET:Pantheon|Nonhuman Deities    ALIGN:NG    DOMAINS:ANY

I copied a line from someone else's and edited it.

Would help to show what you've got in those two associated files too.
Languages.lst needs a TYPE:Spoken.Written tag.
Dieties.lst, your text needs to be in a DESC: tag.

-- 
Dave Klassen
Media, PA

That looks right to me...

Well, this is annoying...  I tried adding my language line to another LST file that is getting loaded but mine still doesn't show up on the list.  I even added another source and its new languages show up.  But when I add mine to that file, it also still doesn't appear.  I'm clearly missing something here.

The PCGen docs say something needs to be added to the skills LST file, but in 5e mode that doesn't seem to be the case and none of the skills LST files mentions anything about languages.

so, I just got your files working ok under 3.5 ... I changed any multiple spaces into tabs (as forum will have replaced tabs with spaces when copy/pasting).
and in the pcc changed gamemode to:  GAMEMODE:35e|Bahamut35e|5e
(that just  lets it be loaded in any of those gamemodes)

Loaded your klassen source alongside my usual 3.5 source and the language appeared under the summary tab as 'add language via skill points' and the diety appeared as expected under domains.
I tried loading 5th ed SRD and got a variety of errors from that source, but with using Bahamuts sources for the 5e core books, your diety appeared ok, but 'add bonus language' on the summary tab was completely blank, so not sure how you're meant to add any languages in 5th ed (Sorry, for 5th ed I've only used an editable PDF from MPMB's D&D 5e Character Tools – Fully automated DnD Character Sheets (flapkan.com) instead of using PCGen so far) no need to add anything to skills.lst for languages (not in 3.5, and obviously 5th works skills differently)

Thank you for this!  I went back to Bahamut's sources and just did a grep for Auran (a language in one of the added sources that popped up) and noted that not only are languages in the xxx_languages.lst but you also have to add a line to xxx_abilites.lst 

Ah! That makes sense, anything 'non standard' can (and should!) be coded up as abilities, that is definitely the way to go.
Glad you found it. I *will* get around to 5e in PCGen eventually...