I found A workaround for the situation.
Our embedded panel has 4 buttons on the left and 4 on the right, much like the NOMADS F/M set.
I had those on the left side anchored Bottom/Left and the others Bottom/Right. By changing them to Left and Right, respectively, they now go where we want them to.
It still seems to me that the original anchors should still be attached to the bottom of the window, where we have the embedded panel placed, and not be affected by the folder's existence at all.