Does it help to save your settings as a project? Also do you use standalone or Acrobat version?
Please send us a sample PDF and before/after sketch. It seems that you can do that with shuffle, but I need to see the details.
Can't you do that with Shuffle mode?
IW got a “shuffle” mode that allows you to rearrange and flip the pages you need. Isn’t it what you want?
Will it be enough to rotate the output sheets instead?
A sample would be great :)