this issues should get a one on one treatment. I have a 001 kit on my desk as well and the revision is Rev *A. Just for sanity check I assume you have a *A as well. So far no issues with programming but my designs are not representative, they are very small, usually just to verify if an issue shows up consistently or on an individual base.
Please create a support case with Cypress.
You can start here: http://www.cypress.com/?id=4
Then create a Tech Support case, lower left corner in the center frame.
Out Tech Support will help you with this issue.
The issue is sorted by upgrading the programmer to version 3.14. Will report if there is problem further!