And just for the record, the issue is related to the implementation of the Tree.js findChild method.
We are using Pathfield, which does have a treePanel object, when calling treePanel.selectPath this calls the findChild function. For an still unknown reason, IE returns a wrong result and the treePanel is not able to select the path, therefore nesting the folders.
That is as far as I could get for now. Attaching screenshots.