Any time this has happened to me, the "missing" window is actually not missing, but hiding behind other windows. And when you do find it, its often nothing more than a small title bar sitting in a lower corner. So, if you lost the MIX window but see the EDIT window, hit the command to bring up the MIX window and check the lower corners(sometimes it helps to shrink other windows). As for missing plugins, open any plugin and place it near the upper left of the screen. Then close it and try the plugin that's missing. On my rig, any plugin I open will always open in the same spot of the previous plugin
If none of that works, right-click on the task bar and try the view options(Cascade windows, Show Windows Stacked, etc)