I did a killing for 1000-1040 in every Hold and paid the fine. But the system didn’t register the trophy. Any thoughts anyone?

Did you had them all at once?
Or did you paid them as soon as you got to the 1000?

ROFFLE! Sorry, but you paid the fines?

Okay, you need to hold the bounty in all 9 holds at the same time to get the trophy. If you did a hold, paid, then went to another, it won't work.

Here's what I did:
I saved my current game, then proceded to a hold. Put an arrow into the knee of the first person I saw, got the bounty. Ran for distance, then FT'd to another hold. Lather. Rinse. Repeat x8. Get award. Load from last save.

Paid the bounty. That was funny.