I have been experiencing an issue where I would arrange a series of Linked Duplicates used as cutting objects for Boolean operations and after saving and re-opening Blender it would place all of the duplicated to match the transforms of the last duplicate I moved. I later realized that this was being caused by the fact that Auto-keyframing is turned on by default and once the keys were deleted, the file behaved as expected.
The solution may be as simple as disabling Auto-keyframing by default. It’s not terribly difficult to disable it of course, but knowing that this is caused by a problem in the Animation tab may not be the most intuitive, particularly to new users.