You're in part mode and you've modified your model somehow, which has caused a feature to fail, so you use clip/suppress. Then when you look at your tree, the arrow indicating where you are in the model has gone to the bottom, after all the features you've just suppressed. If you need to create a feature in order to get the rest of the suppressed features to regen, it will of course be after all the suppressed ones.
I do this several times a day and after using ProE for 12 years. I create a new feature and - woops - it's at the bottom of the tree after all those suppressed ones. "Damn I did it again!" Buts what's even more annoying is I can't just drag the new feature up the tree and place it after the last regenerated one, because ProE won't place the new feature *before* a suppressed feature. Why?
Also I can't just drag the arrow up the tree to after the last regenerated feature for the same reason - ProE won't put you *before* a suppressed feature. WHY? This seems like such a simple thing so I don't understand why it doesn't work this way.