After completing my first GPU WU successfully, i started another which was not checkpointing properly and losing work done.

You will need to update your core to 0.7 to fix some problems with the GPU client. It fixes reporting and checkpointing. There is a minor performance increase also.

You can download it here: http://folding.stanford.edu/release/FahCore_10.v7.zip

Half way through my 2nd WU now and all is going fine!