There have been several replies to the equivalent threads on the SETI number crunching boards, where nevica (using the handle Daniel S. Gandolfo) has posted the same issue in two adjacent threads, believing either the app or his CPU may be at fault.
In fact, the general consensus is that his recently-updated Ubuntu 2.6.24-19-generic (64bit) is running 'nice' processes at half-speed, to save power.
BOINC crunchers have been bitten by this one before, and no doubt they will be again in the future.