Ben, two questions:
If you right click on ArcToolbox and add the FMV toolbox manually from the System Toolboxes does it remain empty?
What version FMV Tool and ArcGIS For Desktop are you using?
I have run into this issue once when I didn't uninstall an earlier FMV version before updating to a new version (I sure didn't save the time I thought I would) . Uninstalling the add-in step by step as described in the user manual and reinstalling the add-in fixed it. The versions were different than you are having an issue with however, so your mileage may vary. You could also try uninstalling the add-in and upgrading to 1.3.1 which will work with ArcGIS for Desktop 10.3 and has some performance enhancements so I'd definitely recommend that if you can . If you continue to get the empty tool-box there may be a deeper issue and I'd contact Esri tech support directly for deeper trouble shooting.