I'm not sure what I have been doing wrong but sometimes when I save my file and re-open it the objects are all displaced in random rotations and locations. My most recent model has been completely scrambled.
I solved it by deleting all of the keyframes, then selecting all objects in object mode and clearing their current transforms. It turns out I had Auto-Keying enabled in the Timeline by mistake which I realized when I saw the locations, rotations, and scales were orange instead of yellow.
As to why these displacements only take effect upon loading I have no idea...