I discovered why this is occurring, quite by accident.
This occurs on computers that have touchscreens. That's why in happens more often on tablets then desktops.
When you boot the computer from scratch, It takes a moment to initialize the touchscreen, so for a while, as far as the OS is concerned, there is no touchscreen present. So when Start11 starts, in this period, it assumes there is no touchscreen present.
When you have "Taskbar Touch Screen Detection" set to "automatic", Start11 ends up in setting "not touch mode device". If you set to "Force Touch Mode Device" On computers that have touchscreens, the mis-alignment problem goes away.
Hope this helps.