A recompile won't fix it. Window programming hasn't changed much since OS 1.x. There is no way for a program to influence window border drawing. Therefore it is also impossible for a program to partially disable VisualPrefs and/or Birdie.
Most likely the program opens a borderless window and does all drawing by itself. This is very untypical and as a beginner you probably won't be able to "fix" it. (There is nothing to fix, the developer intended to let the window look like that. You would have to rewrite all the code.)
