So I created this project earlier today, it was working fine. Went on to something else then came back to render and all my objects are stacked. The Loc/Rot/Scale is all reset visually but the values show up correctly. If I try to move any of them, the values update but visually it stays in the same place.
Also, applying transforms visually kind of fixes it. They go into the same grouping/spacing as they should but in the wrong location. If I then set the origin to geometry they restack themselves.
Also, they are not reacting to physics as they should. No animation in this version whatsoever.
I created another project and started over and am having the same problem. Not only that but resetting the timeline doesn't reset the objects/physics, they keep animating as if the timeline is much longer.
I had to dumb down the blend file a lot in order to upload, so only one object. But it should get the point across.