I am having a problem where whenever I enter a shop, the shopkeep comes running up to me like I have a bounty or I stole something from them. But I check and I have no bounty. Then I walk past a guard and they don't arrest me. I can even talk to them and nothing happens. The exact same thing happens in the Shivering Isles world. It is really getting annoying...

Try manually setting yourself with a small fine, then paying it off or going to jail. Whatever is causing the issue may work itself out. Any mods which affect crime or NPC behavior may also be responsible.

I've commited plenty of crimes over the duration of this, and have payed each off in due course. I also don't have any mods like that. Thanks anyway. You know, it is kind of convenient to have the merchant come to you...