[BaseFaction
faction = li_n_grp
weight = 13
offers_missions = true
mission_type = DestroyMission, 0.000000, 0.112387, 30
npc = li0101_lnavy_001_f <-- Check and mark sure your npc has add here. maybe Freelancer will enumerate the value and found npc.

[GF_NPC
nickname = li0101_lnavy_001_f <-- make sure the npc are exist
body = li_female_elite_body
head = pl_female1_head
lefthand = benchmark_female_hand_left
righthand = benchmark_female_hand_right
individual_name = 220007
affiliation = li_n_grp <--- take look^^
voice = rvp511
misn = DestroyMission, 0.000000, 0.112387
room = bar <--- make sure your npc in correctly room
...........................



and if bartender not in the bar

[MRoom
nickname = bar <--- make sure your npc in correctly room
character_density = 7 <-- depends on THN file
fixture = li0101_fix_bartender, Zs/NPC/Bartender/01/A/Stand, scripts\vendors\li_bartender_fidget.thn, bartender <-- make sure your bartender are exist (exp. li0101_fix_bartender)




and about mission. did you mean your new faction not give you mission? maybe you need to check empathy.ini and add your new faction to VignetteParams.ini

It's Odd... Every time I open FLE it adds a Duplicate Entry to both Mbases.ini and Universe.ini: Li01_01b_Base.
It's a Pain, and I' simply get rid of them as I go along.
Also, could market files affect all of this?

Sound to me like you have either an old version of FLExplorer or a corrupt one from a crash. Uninstall that puppy. Here is a link to the newest version, 2.0.6.23 (which will show up as .22 internally);

http://eoa.seriouszone.com/colinsanby.php#flexplorer

Now, I'm sure if this is related to your problem....
but recently I discovered I could not make changes to a certain file
until I made sure its properties were NOT read only.
I could have saved myself a ton of grief if I had changed its properties
at the start.