Thanks... I suspected a hardware issue with both of the boards and even have large number of FreeIMU boards which I added to some panels of PCBs I originally did for another project. My plan was to build them up and see how it differed from the ArduIMU. I just checked the FreeIMU layout and you are correct that there is copper on the back side of the board under the compass. I don't think I will pursue either of these boards right now.
Are you doing anything in your software that isn't being done in either the ArduIMU or FreeIMU software that would improve on the performance, namely yaw drift/accuracy. BTW, I don't really care about roll or pitch in my application and, in fact, hope to fuse GPS heading data into the calculations at some point. My application is described here: http://freeimu.varesano.net/node/47.
When will your IMU board be ready? I do a significant amount of embedded design including layout, build, and test. I am happy to help out/collaborate in that regard with your new designs if you wish.