Skyrim, Stormcloaks Keep attacking me (I AM A STORM CLOAK!)

Hey guys, I don't know if this is the proper place to put this but whatever,...

I've been getting into skyrim and I'm deep into the stormcloack story line.   When I go up to soldiers in a camp or windhelm, everything is just dandy.  But when I'm in a quest to take over a city or a fort, all of a sudden I'm the enemy.  I've went back to windhelm, payed whatever bounty I had, talked to the Yarl ulfric but still. I find it quite difficult when I'm capturing a fort and both the storm cloaks and imperials are trying to attack me.  

Anyone have any suggestions please?  I have mods, i'll post the list if it's necessary.  

Fuck yeah! Stormcloaks!

Perhaps pick up the armor disguises mod. That way when you're wearing full SC armor they won't attack you... PS the war system thing in Skyrim is a huge disappointment.