I'm experiencing the same problem, but only when using versions 3.6 and higher. The problem can be avoided if all the temps are set equal. However, it would be better if Cura would reactivate the current extruder after setting the previous one to standby temp. That can be done using the same command but using T1 instead of T0, if the current extruder is T1. For example, turn this:
M82 ;absolute extrusion mode
; tool end script
G92 E0
G1 E-6 F10000 ; retract to prevent stringing
;G91 ; switch to relative positioning
;G1 Z1 ; travel +1 on z
G90 ; switch to absolute positioning
M82 ; ensure e is absolutely positioned
G1 X24 Y15 {travel_speed} ; move to 10 0
;G92 E0
;G1 E6 F2000 ; undo retract
;G92 E0
;G1 E-5 F2000 ; stage 1 of 3 stage retraction
;G92 E0
;G1 E2 F2000 ; stage 2
G92 E0
G1 E-58 F3000 ; stage 3, this keeps from producing "hair"
G92 E0
M83 ;relative extrusion mode
T1
M82 ;absolute extrusion mode
; tool start script
G92 E0
G1 E59.5 F2000 ; return - 1 to keep nozzle from oozing
G92 E0
M83 ;relative extrusion mode
M104 T0 S170
into this:
M82 ;absolute extrusion mode
; tool end script
G92 E0
G1 E-6 F10000 ; retract to prevent stringing
;G91 ; switch to relative positioning
;G1 Z1 ; travel +1 on z
G90 ; switch to absolute positioning
M82 ; ensure e is absolutely positioned
G1 X24 Y15 {travel_speed} ; move to 10 0
;G92 E0
;G1 E6 F2000 ; undo retract
;G92 E0
;G1 E-5 F2000 ; stage 1 of 3 stage retraction
;G92 E0
;G1 E2 F2000 ; stage 2
G92 E0
G1 E-58 F3000 ; stage 3, this keeps from producing "hair"
G92 E0
M83 ;relative extrusion mode
T1
M82 ;absolute extrusion mode
; tool start script
G92 E0
G1 E59.5 F2000 ; return - 1 to keep nozzle from oozing
G92 E0
M83 ;relative extrusion mode
M104 T0 S170
M104 T1 S200