The line you said you changed is only used for a testing mode where the
kinematics are run as a standalone program. (#ifdef MAIN)

When running as a part of emc2, kinematicsInverse sets fflags depending
on the world coordinates.  If you are at a world coordinate with
negative z, it will assign *fflags=1, but for zero or positive z it will
assign *fflags=0.

Perhaps the modification you need to make is to prefer *fflags=1 when z
is exactly zero, and/or make the home position be strictly negative in
z.

Jeff

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