Okay, now this Markarth glitch is starting to get irritating. The guards do regenerate between visits, and since the bounty keeps getting higher without any means of clearing it, that means more and more guards keep coming after me. I can't even fast travel to the city without immediately attracting their attention.
How much is your bounty now? If it's an irreversible bug just make the most of it and go for the 'xxxxx bounty in each Hold' Achievement.
EDIT - I know of one way which might clear it but that depends on how far in the main quest you've got.
WARNING: "if you've not done Season Unending don't read" spoilers below
It's a long shot but if you convince the Imperials to give Markarth up to the Stormcloaks, they get a new Jarl and new guards. It might reset their hostility, but it's a total guess on my part
__________________
"Critics are like eunuchs in a harem; they know how the Tatty 100 is done, they've seen it done every day, but they're unable to do it themselves." - Brendan Behan
"Critics are like eunuchs in a harem; they know how the Tatty 100 is done, they've seen it done every day, but they're unable to do it themselves." - Brendan Behan