Make sure you have every Matter Manipulator mode unlocked: You don't necessarily need every upgrade, only the basic modes (mining, wiring, inspection and painting). If all four of those are unlocked, simply press the left mouse button while holding your Manipulator Override, and you'll get the new skin applied to your Matter Manipulator.

Yeah, It isn't working for me either.

There's multiple ways.

1: you just need /admin.
And the will to upgrade your manipulator all over again.

/giveessentialslot YOURRACEbeamaxe beamaxe
/giveessentialslot YOURRACEpainttool painttool
/giveessentialslot YOURRACEwiretool wiretool

You're supposed to replace YOURRACE slots with the name of your character's race.
Examples, trinkbeamaxe, avikanbeamaxe

2: You might just need to unlock it "properly".

for example the Avikan/Droden version requires you to go to Captain Zaheed.
I did that and it worked for me all of a sudden.

3: Probably the easiest,
you might still be using a magnifying glass instead of the scan tool.

Get the Scan Tool from the learning about the outpost quest.