Not show the correct joints

Which LinuxCNC version?

Are you still able to jog every axis that you need to jog in Joint mode?

There is actually scope for debate about which is the correct way to number the joints, the latest version of 5axiskins in the development branch specifically maps X-0, Y-1, Z-2, B-3, C-4, W-5 because it makes no sense to have gaps in the joint numbering sequence.

To be honest, I think that all the developers are probably too busy at the moment integrating some major changes into the 2.8 version to pay much attention to a problem in 2.6 _if_ it is purely a cosmetic problem that doesn't prevent operating the machine.

Well, the big change that the devs are now working on is the joints-axes merge. This has been in the background for years, but has finally made it.

In the next version of LinuxCNC "Axes" XYZABCUVW will be completely separate concepts from "Joints" (ie, motors).

A typical lathe, for example, will have X = joint 0 and Z = joint 1. No dummy Y-joints as is now required.

So, an XYYZ router could have X = 0, Y1 = 1, Y2 = 2, Z = 3. Or any other combination. The system won't care which motor moves which joints. This should be a huge improvement for systems like robots and gantries where there is not a 1:1 correspondence between cartesian coordinates and actuator motors.

So, in LinuxCNC 2.8 your machine would have joints 0,1,2,3,4 and axes XYZABCW. (I imagine that you do not have an actual W-axis actuator?)