Please be aware that multiple queues is not supported in 1 instance of a call to clfftEnqueueTransform. You MUST call clfftEnqueueTransform 2 times (passing in 1 queue each time) if you wish to use 2 different queues.
People have successfully used the library with 2 or more queues (each associated with different GPUs) to parallel process provided they call clfftEnqueueTransform appropriately. It is not explicitly clear from your post that if you are using multiple GPUs, or just multiple queueus on single GPU. If my answer is not clear, please let me know. If you have code for me to look at, I can point out the error pretty quickly.