do you have customised versions of the LM_tools installed? A tool can be installed but absent from the Tool window - there's an "IsRelevant" function that a tool used to decide whether or not to show itself in the tools window.
I would try pointing the Custom Content Folder to a new empty folder. This will generate a default folder you can use to check whether the problem is with your current custom folder or something else.
After setting the new folder, press Ctrl+Shift+Alt+L to reload the settings from it, or simply quit and relaunch Moho.
Is the tool available now? If so, then this likely means something is broken in your old custom content folder, or there is a conflict with a third-party script. From here, you can add your custom tools and assets to the new content folder gradually to test their compatibility. When you're done, you can delete the old folder.