I know this is old and marked as solved, but I thought I'd add this information here as it was the first topic returned in the search on "cpd is corrupt".
We started getting this message on a project we had copied to create a new project. It was confusing because the original project didn't suffer this problem, only the copied project.
After much searching we discovered it was because for the copied project, a blank rhvariable.apj file was created which didn't exist in the original project. (I assume because we deleted the cpd, pss and sss files and deleted the source control information out of the xpj file - not sure why it wasn't created when the project was upgrade to RH6 from X5...)
The solution to the problem was to add content from a working rhvariable.apj file. Voila, no more "the cpd is corrupt" messages.
The code for a blank variable file in RH6 is:
<?xml version="1.0" encoding="windows-1252"?>
<rhpml majorversion="1" minorversion="0">
Hope this helps someone in the future.