This is a crazy bug that occasionally showed up in versions 12 and 13. It was finally corrected in version 14.
Beyond that, I'm not aware of a fix for versions 12 or 13.
Have you updated 12 to 12.1 yet using an opened project's Help Menu/Updates?
I have Premiere Elements 12/12.1 and 13/13.1 and 14 on Windows 7 64 bit and Windows 10 64 bit and have not run into the problem that you have described.
Consequently I am not seeing any 12/12.1 and 13/13.1 issues of this kind fixed in 14.
I suspect that the issue goes to the specifics of your workflow rather than a bug. But, to prove it to yourself, have you considered (for troubleshooting purposes only) downloading and installing the free 30 days tryout of 14 from Adobe and giving it a workout under the same conditions that exist for 12/12.1. You do not have to uninstall12/12.1 to do this. Just use one version at a time.
Also, could you describe the complexity of the Timeline that exists when this issue presents itself as well as the type of edit involved at that time?
I have experienced what the original poster is seeing on a number of occasions, on both the Mac and PC versions of the program.
I guess it's up to Erik to decide if the problem is with the program or with his system configuration.