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Dual Extrrusion with Per-Layer Temperature Setpoints

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Hello everyone.
Trying to perfect my dual printing. The model I'm trying to make has a section near the top that's a different colour than the rest. By default the printer wants to heat up both extruders at the beginning. That results in one extruder idling hot for an extended period, which is bad and ends up ruining the print when it tries to do it's part with 'baked' filament. So s3d has a 'per-layer temperature setpoint' setting which I figured would be exactly what I need. It works great if I make the temperature changes at the beginning of the print, but all the changes at the end, where I need them, are ignored. Does anyone have any idea what the problem might be?
Thank you