Option 1: Disable "Launch WM Toolbox when World Machine starts". Completely exit World Machine by right-clicking the G icon and selecting EXIT. Then start it again from Programs. Try loading WM Toolbox manually. This should fix the problem in most cases.
Option 2: If Option 1 does not work, please change the Dock position in Options from Right (Default) to Right (Side-by-Side). Restart GeoGlyph as mentioned above, and try loading WM Toolbox again.
We recommend using only one instance of World Machine at a time, other WM Toolbox may fail to recognize the current running copy.
If both options fail to solve the problem, please contact tech support.