I also have found all 0's in these measures when I try and run the entire year. If I run 3 months at a time it counts the CQM measures properly.
It seems to me that it must be timing out before it gets to the CQM measures. This MUST be fixed. I attested in 2011 and I have to keep going this year. I believe that once you start you must continue or they can make you give back the money you already received.
If this isn't fixed before the end of the year I will print out quarterly reports and try and put them together and attest with the numbers that I get by this method.