I believe I have encountered this same issue repeatedly in my e17 setup.
My dual-screen monitor configuration is horizontal rather than vertical, but the symptoms are the same. After e17 crashes or restarts for whatever reason, my left and right displays get swapped (which is particularly annoying since they are different sizes and resolutions).
Note that I don't use gkrellm (it's not even installed on my system), so I suspect your clues focusing on gkrellm were misleading.