No. The Functional View is built from dynamic data (i.e. based on the applications registered with Cisco Management Information). This data is stored in a format which promotes quick look ups rather than linear searches, and thus may be loaded in a different order each time the Portal initializes.
As a workaround, you can create your own View, add the portlets you want in the order you want, then set that View to be the default. The order should then not change.
