Hal encoder bug?

Does it have to be M6?
If you can put up with using
O<toolchange> CALL 5
to load a tool then you could put the actual M6 command and a probe - touch-off in a subroutine.

There will eventually be a way to define a G-code routine to be called by M6 (ie, it is there and working in the 2.6 branch) So the G-code will have a standard-looking M6 T5 in it, but the toolchange will be a sequence of G-code commands.

You can see an example of how it would work in the demo config here:
git.linuxcnc.org/gitweb?p=emc2.git;a=tre...22843eba66a1fd23d94e
(The owordm6-ui.ini file)
But I don't think it will work unless you download and compile the development version.

2.5 isn't out yet, so I would imagine that 2.6 is probably 6 months away.

I don't think that those changes are due in 2.5.