I recently had this issue on 2011 Vanilla deployments. I ended up exporting the tool palettes out from a machine that I had installed directly from the DVD. Then import them on the machines that I used the deployment on. Quick fix, but it should work right to begin with in my opinion.
Brent Daley
Civil Designer/CAD Services Manager
The Land Group, Inc.
Civil 3D 2016 SP1
Windows 10 x64
Core i7 3.40 GHz 8gb RAM