I only can align my folders when I remove the file underneath and open another folder. When I have already a file under the previous folder, the folder aligns with the file and not the folders.
There is also an instance where a folder starts more to the left as the other folders. Here is an example:
Folder (how it should be)
File (how it should be)
Folder (how it shouldn’t be)
Folder (how it shouldn’t be)
For all of the details on how to move items around in the binder outline, refer to §6.3.4, Moving and Copying Things Around, in the user manual PDF. There are several different techniques, because we know everyone has different preferences here. If drag and drop isn’t working for you because of its lack of precision, then maybe something like the keyboard shortcuts that only move one step at a time will do better (that is my preference in most cases).