Perhaps the kernel pushes your card harder and it generates errors. But could be the pool, driver and so on, like Vince said.
Dia
Stales have nothing to do with GPU errors in Phoenix. All results returned by the GPU are verified before being sent to the server, which means if the kernel finds invalid shares you will get "Unexpected behavior from OpenCL. Hardware problem?" instead of the share being submitted. If you are not getting any of these errors there is NO WAY a kernel change can affect the number of stale shares. It might affect the total number of shares submitted in a given time period, but every share sent to the server by Phoenix is verified to be H == 0 on the CPU beforehand.