I have never had this much trouble with a game from Bethesda.

I just finished the Liberate Skyrim questline, with the taking of Solitude for the Stormcloaks, and now every time I go into Whiterun I have guards swarm me saying that I've committed crimes against Skyrim. I was even attacked by the new Jarl who was saying "for your accomplishments in battle I will now allow you to buy propery in Whiterun" as he's attacking me. If I go into the Blue Palace in Solitude, I get swarmed by guards there.


Has anyone else had to work with this problem?

After completing the Stormcloaks line, I have had some strange bounties I had to pay. Really minor amounts, but I wasn't really sure what I did to piss them off. I still have a problem in Markarth. They won't take me to jail or let me pay them, so I have to kill them every time I go there.

Yeah the game is a little bugged.Do you have a previlyous save?if yes,reaload it.I always have more than 6 saves when i have these problems.xD.Also i experienced 2 problems like these.On falkreath and in markarath.
In falkreath is intersting because it's like a glitch,every time i see a guard they acuse me of murder,than i use my persuade to level up the skill fast =D

It is hard to tell the good guys from the bad guys in that battle. You may have inadvertently killed a Whiterun guard or two and incurred a large bounty. Have you checked stats to see if you have a bounty?