Every time I try to go to SI I get accosted by the guards and either have to go with them or fight them, being not allowed to pay the bounty of 5200 or so gold.

Is there any way to fix this glitch? So far I've just been slaughtering the guards when they attack, but now civilians are getting thrown into the mix and a depopulated isles somewhat takes away from the immersion.

Also in my journal it shows me as having no bounty in SI.

Are you running any mods?.

FCOM and then mostly just armor and house mods.

you dont pay bounty in shivering isles..

the reason why is on one of the loading screen hints.. you get taken to a dungeon whatever your crime.

I would recommend just going to jail. Its not that hard to break out.

Every time I go with the guards they dump me outside the city gates and when I go back in they just arrest me again.

I have never heard of this before. Do you have any clue at all as to why this has happened? For example, it was fine before you went on this quest but when you came back...

Go to jail then