I'm on the PC and sometimes (about every other time or some odd pattern) when I go to Markarth the guards attack me. During the Forsworn Conspiracy I never touched any of the guards, yet this problem still happens to me. Once I waited 48 hours and came back, and no one attacked me, but now it's started up again, so I can't talk to Muiri and it's really getting annoying now... anyone else have this problem?

Did you complete the Forsworn Conspiracy quest and the next quest involved with it, if you did then the guards probably didn't reset the bounty. Thankfully your on PC so you could use the console to fix it although I'd make sure your putting in the correct numbers or else you'll be spamming 1000 chickens in the middle of the city.

http://www.uesp.net/wiki/Skyrim:No_One_Escapes_Cidhna_Mine

This could help too although I'd make sure to save beforehand if you try anything.

Atfer the Forsworn Conspiracy quest there another quest you have to go back to talos shrine in Markarth the guards will take you to jail and the other quest will start.

LOL @ chickens comment. Well, I already did the whole break out of jail thing...I guess i'll just wait and see if it clears like it did last time. If not I will have to console it. Does it save? or would I have to do it every time I load my game?

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I will move this now.

What bothers me is that not only did I let the guards arrest me; but I never harmed a fly when we escaped with Madanach. I simply waited at the exit for the Forsworn to finish their rampage, and when it was all over, everything was fine. But now, every other time I go to Markarth the guards attack me...yet i've fixed it once by simply waiting 48 hours of in-game time. This whole thing is weird...oh well. I'll use the console as a last resort if it keeps acting up I guess.