The generation of the PEK (Waveform Display) files (also the CFA, or Conformed Audio Files) is something that should be done once, when the Asset(s) is/are Imported into the Project. Those files should be linked in the PREL file, but it appears that they are not. That does not bode well.
First, have you tried to do a Save_As for the Project, creating a new PREL file? I would try that, and just name that one something sequential, such as [Project Name]_01, noting the exact location of that PREL. Does that Save_As file now Open properly, with the PEK and CFA files linked properly?
If not, then I would do a complete survey of my HDD's (Hard Disk Drives), as something might be wrong there. Are you having any other issues with corrupt files on that HDD?
Are you perhaps trying to Save to a USB 2.0 external, or to a networked, or Mapped HDD? If so, I would list the full I/O sub-system with the drives, their connection type, and how you are using them, as someone might see an issue, and be able to make suggestions on how to avoid it.
Please supply the following information to help us to factor in or out possible causes of your Premiere Elements 12 workspace issues.
1. Go to Edit Menu/Preferences/Scratch Disks and tell us where each of the categories is directed to. Also, how much free hard drive space is at that location.
2. Then go to File Menu/New/Project and tell us what you see designated in the Save In field of the new project dialog.
3. If you go to Libraries/Documents/Adobe/Premiere Elements/12.0, what do you find in each of the folders in the 12.0 Folder? Are there any files in the Adobe Premiere Elements AutoSave Folder?
We will decide what next based on your answers to the above.