Sometimes your current bounty is just too high, and they just instantly and incessantly keep attacking you. It svcks, but they also tell you about this possibility in the loading screens at times.
Like Haleand said, run away until the guards aren't chasing you any more, and then fast-travel right back to the same city/town that you were running from. The guards near the front gate (where you conveniently appear), should immediately go into uber-machismo arrest mode.
And then your bounty gets cleared up.
