Sorry to be (VERY) late to the party, but I'd just like to give another solution for those still experiencing this issue with their bases. I'm honestly surprised nobody has proposed this one yet.
This solution uses KAS. If you place something on the floor, H + LClick will bolt it down, and make it unmoveableunmovable. This is useful for something like Pathfinder, where you assemble bases with KAS.
If you've already landed something and just want it bolted down, you can attatchattach CC-R2 Connector Ports to the base. Then bolt down (H + LClick) one Ground Pylon or CB1 Ground Base per port. Add a connector port to the Ground Bases or Pylons. Link the connectors together via their RClick menus and that will bolt the base down.
It should look just like Bill Kerman's demonstration here: