It's all right, they don't interact. Banter accelerator deals with banters only - there's a built-in script for that. Scripted conversations or flirts are not affected at all.
Well, I just thought that the romance interactions that come with this mod which happen automatically might "count" as banters. If you set the banter accelerator to 45 minutes and these talks happen more frequent you would never gonna see any more banters. But, yea, this seems nonsense...
If any banter from any mod triggers more than once, it's possibly a bug which needs to be reported. If you post the actual string(actual words), it'll be helpful - we'll find out if it's NPC Flirt or some other mod.
As for the rest, I'm not sure what exactly you mean. Do Banter Pack and NPC Flirt Pack work together? Yes. Are they supposed to work with other NPC mods, like NPC IEP? Yes. Can there be bugs? Yes, if a modder forgets to put his WEIGHT commands in, but I'm not aware of any major conflicts for now.
Maybe this is stupid but: Is the romance talk from this mod which starts from time to time somehow in conflict with the npc banters? Do those talks count as banters and therefor prevent banters from starting? Or is it something completely different and doesn't affect the banter talks at all?