I recently came across this phenomenon:
In an instance of VI instantiated within VE, I turned Velocity X-Fade on and assigned CC11 to Velocity X-fade.
After having saved and re-opened the file, velocity X-fade was still turned on but, in the Map Control window, "None" was the control assignment for Velocity X-fade. When I looked at the list of controllers under the flip menu, I could see that CC11 was selected. To get it to reappear correctly in the Map Control window I had to reselect it.
This behavior contrasts with what happens when a VI instance is instantiated in Logic 8 and the file is saved. All settings remain as they were when the file was reopened. I hope this will be addressed as it is very laborious to go through a large template and redo the control mapping for each parameter that may have lost its mapping.I will test with other parameters and controllers.