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There are two things to check:

  1. You need to select the APT process which the Dub with the Protected Region is the input to. (You most easily select an APT process by clicking either the Dub Process Control Block or the Output.). It will become green and the process information panel at the right of the track should show something like "APT:2 Dub Energy".
  2. If it does NOT say “Energy”, then you need to open the APT control Panel for that process and select "Energy" in the "DISPLAY/EDIT" section.

When those two items are taken care of, you should be able to select the handles at the top of the Protected Region and drag them.