The problem was the update was not executing because it did not notice a change in the build. I created a simple build.txt file that held the build number. It is a little different from the example in the blog that is referenced, I created an actual file rather than just changing the metadata. http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/cfn-hup.html
"AWS::CloudFormation::Init" : {
"config" : {
"files" : {
"c:\\cfn\\build.txt": {
"content" : { "Fn::Join" : ["", [
{ "Ref" : "BuildNumber" } ]]}
},