My chicken pot pie sauce keeps separating when frozen..help!

What are you using to thicken the sauce? University of Illinois Extension has a good guide about what to use:
http://web.extension.illinois.edu/state/newsdetail.cfm?NewsID=3231

Did you use flour as a thickener? If so, then that's why your sauce separated.

It's going to help a lot if you give the method you use to make sauce. And maybe describe what is separating from what.