Spindle synchronization problem. Help please.

Hello, we recently started working on a 3-axis cnc drill using linuxcnc. The basis of the machine are 3 axes and a spindle with a 4-speed gearbox.
We use MESA cards 7i76e as the base card and 7i85 as the card for the spindle encoder. The spindle encoder is located on the output shaft of the gearbox and has 360 pulses per revolution and 1 index pulse. We have a remapped S command which changes the gears in the gearbox based on the set speed. This works for us without any problems. Plus we have active PID spindle speed control that works excellently. If we select the speed, the S1000 gearbox engages 2 gears and the PID controller adjusts the analog output on the inverter so that the actual speed is also 1000rpm. As I say, we have no problem with this. The problem starts when we want to cut threads with G84. Example program:

G0 X100 Y100 Z5
S100
M3
F125
G84 Z-10 R5
X0
Y0
M5
M2

Units in MM.

The threading cycle starts but the axis feed is not synchronous with the spindle speed.

On our CNC milling machine where we have a FANUC system, the spindle is first positioned during threaded cutting and the Z axis feed is started when it is in motion.

However, this is not the case with our linuxcnc drilling machine. I don't know where the problem may be, can you please advise me? I am very grateful for any advice.

Well thank you.

Have you tried without a remapped S command?

@Mods:  I think this topic fits better in the category "Configuring LinuxCNC -> HAL" as it is not Gmoccapy related.