I noticed something strange happening with a few of the encoders, after power up, occasionally some encoders would report an incorrect position, usually with and error around 90 to 180 degrees. What was strange was that if the encoder was moved slightly it would snap back to the expected position!
Having spoken with the SICK technical rep today, I decided to break out the scope once again and look at what was happening on the bus. Sure enough an encoder in an error state would suddenly flip back to its expected state when moved slightly as confirmed by monitoring the bit stream on the scope. At this point It was looking like an encoder fault, which was slightly worrying, however, I decided to slow down the clock rate to 450Khz which had been running at about 800Khz. This seems to have cured the issue, which is a little odd as the encoders SSI bus is supposed to run up to 2Mhz.
I have yet to discuss this further with the technical rep, but as long as the issue goes away I'm not to fussed. It could be something to do with cable lengths / termination etc.