Preheat oven to 375F. Spray a 2 quart casserole dish with non-stick cooking spray.
Melt butter in a small saucepan. Add onions and jalapenos to pan; cook for 5 minutes or until tender, stirring frequently.
Add flour to butter mixture, stir for 30 seconds. Add milk, chicken base, and spices. Cook over medium-high heat stirring frequently until sauce thickens. Remove sauce from heat.
In a large bowl combine potatoes, sauce, sour cream and 1 ½ cups shredded cheese. Mix well and pour into prepared casserole dish.
Bake at 375F for 30 minutes. Remove from oven and top with remaining cheese. Bake for an additional 10 minutes or until cheese is melted and bubbly.