Meshes and bones rearrange seemingly randomly?

This is my first post so I hope I’m in the right place. I am using Blender 2.60 (r4226) and as of a few days ago my project file and backups have been acting really weird. I have an image below for reference to what it’s supposed to look like.

Issue #1: Each limb is a separate mesh since that seems to animate the best (for me) in this scenario. If I close Blender or sometimes even sleep my laptop a couple of the meshes will rearrange themselves back to the the original shape it was mirrored from. All parameters for L, R & S are locked so best to my knowledge this shouldn’t be possible.

Issue #2: The action I created for the right hand grip is spontaneously deleting itself or in some cases renaming bones back to the original “bone.0xx” format. This obviously prevents me from using the action nearly 70% of the time.

Issue #3: (A new one that just came up last night.) One of the armatures for one of the character deformed itself in a very odd way. In edit mode the armature was still correct, but in pose and object modes the armature was deformed and scaled on all but the crouch and hip motion bones. In this case alt keys would not restore the original either. All bones have scaling locked so this should not be possible.

A little background on the project:
I have 5 characters and 1 scene in the same blend file, as well as close to a dozen weapons. It’s a ton of data! I’m not sure if that is part of the problem. It’s a project I have been working on for a couple of years, a few of the meshes were created in 2.49 and transferred over which messed with the normals an some of the parenting. For this reason if I can avoid upgrading blender I would much prefer that option. However I do suspect this may be an issue with 2.60, though Google and forum search have yielded no results. Help is greatly appreciated!