We spotted also some similar problem but it's a bit different from what Fridge encountered:
We wanted to buy a base under "The Generic Ass Kickers". The dialog appeared and i told him this name. No caps were taken from inventory and the dialog didn't go further. Even though it seemed that this name isn't working, we checked the w-map quick, if there was some new base to be seen somewhere. There wasn't. So we tried again, this time under the name "The Skullz". This now worked and the caps were withdrawn etc....
Now the strange thing is --> If you look up the terminal it says "The Generic Ass Kickers"
This wasn't the faction we choosed or at least which didn't work in first place. When you try to "manage hideout.." there it says "The Skullz", which was the faction name, which finally worked.
I think, in this case you haven't read the dialog properly:
1) You chose faction name, faction had been created, dialog got interrupted.
2) You thought faction had not been created (because there were no base (it had not yet been bought)), so you wanted to buy another by creating another faction
3) You went to NPC, but he asked you about base name, not faction name. You entered The Skullz, which created the base that had been assigned to The Generic Ass Kickers.
Like in my previous post - it's possible due to the ability to create faction without buying base (by interrupting dialog).