I called "GPUPDATE" today, but nothing's flickering here while that tool is being executed.
To me it seems like the guest OS pauses running while the screen is black. The black periods are particularly long at my slow machine or when my SSD drives are busy copying large files.
VMware, wouldn't it make sense to add profiling/auditing/stop-watch calls to each of VMware Tools' API entry points while you're debugging? The first flickering in a guest session always occurs when VMware Tools finishes booting in the guest, so it should be easy to find the call that's causing this flickering. (Strange enough: It doesn't occur when I restart the VMware Tools service in the guest.)