I recently joined the thieves guild. I had an option in Riften to only pay 2 gold pieces for my fines. In dawnstar and windhelm, I got a 1,000 gold bounty and had no such reduced option fir this bounty. Am I missing something?

i guess its because there is no 'influence' in the other cities yet.

Good point

I've gotten out of paying fines being the thane of whiterun, I assume it would work in other cities too.

iirc, when youve finished the special jobs, you will probably find you can lower them everywhere.

This is interesting. I had a dialogue line "I'm with the guild" when a guard caught me in Dragon Bridge, but the amount of gold I'd have to pay was actually higher than the bounty. I had only done one job in Haafingar before.
Maybe with every job in the hold the amount of gold you're asked to pay decreases?

I even tried going back to the flaggon to see if someone there could help, but nada.

sounds right, i guess