I hope it's not something like that. I sided with the Imperials but I don't remember what happened to Markarth along the way. I had no problem getting jobs in Windhelm though.
I'll probably go build my Hearthfire houses and finish my werewolf perks and then go back and see if anything has changed. Just through Googling I've found some people mentioning this same problem (with different cities, so it's not specific to Markarth) but I haven't seen any answers except "wait a while and keep trying."