Tuning stepper motors with encoder or glass scale feedback

what do you mean by a configuration problem, in a .hal file?

Homing configuration is in both the hal file (index and home switch handling) and the ini file
(type of homing, directions, speeds etc) 

linuxcnc.org/docs/html/config/ini-homing.html

Are you saying that my .ini file is misconfigured and that's why I can't detect my Z homing?

Did you check the home switch operation?

That is, does  joint.2.home-sw-in go true (change from red to yellow in halshow)
when you manually trip the home switch?
 

my configuration works very well on the x,y,z axes with on/off switches. homming is all done at the same time without any problem. the problem is only on this rotary axis where i have an encoder with which i want to use the Z phase to do my homing.

OK, that's probably to be expected since there does not seem to be any B axis home switch
and you have setup a homing scheme that requires that switch.

If you don't have a home switch on B, and you want to home to index, you need to setup
Index-only homing:

linuxcnc.org/docs/html/config/ini-homing.html#_configuration