Everytime I load up Fallout it overwrites my current Auto-save with one from 36+ hours ago. I have tried deleting the auto-save from both inside & outside of the game and this old one keeps coming back. Thankfully, I haven't experienced a crash where this has caused me to lose work but I'd still like it fixed.

I've had this problem before. Are you using Steam? If so, look at my posts, I have a method that's solved my problem.

I am using Steam (like there is any other choice on the PC, lol) and I tried your fix with no success. This save still automagically returns out-of-nowhere overwriting my current auto-save upon game start-up. Interestingly enough, it's date/timestamp is the moment it was overwritten like it was re-written from scratch rather than copied from somewhere else.

Are you sure Steam Cloud is disabled and you are patched?

Check Steam -> Settings -> Downloads + Cloud and untick it if you haven't already.

Also some of us believe that since Oblivion the engine is more stable if you turn off all the auto-save options and just manually save (a lot!).
No real downside in doing this really, except when you forget to save for two hours and it crashes

This bug was fixed by the patch that was released last week (which auto-disables the Steam Cloud, so you don't need to bother with that yourself).