Missing M104 in gCode for multi material print  

Missing M104 in gCode for multi material print

I originally posted this in MMU2 sub-forum but realized it should probably be under PrusaSlicer forum instead.  Apologies if you read it twice.

We have had this issue for awhile but it is becoming more urgent to fix.  This is for a MK3S+ with MMU2S, current PrusaSlicer, current firmware.  If we have a model with 2 preset filaments (say Atomic and Hatchbox) as in the attached example, and if the different filaments are both evident on the first few layers, and then after that are just one or the other filament on a particular layer, the temperatures are not being applied correctly.  This doesn't matter tremendously if the PLA filaments are close in temp, but does matter if one is regular PLA and the other is PLA+ or Silk PLA etc.

In the example Atomic PLA is 220/215 and Hatchbox is 215/210.  I have a sample part that has a blue circle for 2 layers (Atomic) inside a green square (Hatchbox). From 1mm to 2mm I use Mod Mesh to make those layers Blue.  So the print proceeds as follows:

• Atomic layer 1 prints correctly at 220. 
• Hatchbox layer 1 then prints correctly at 215.  
• Hatchbox layer 2 then prints correctly at 210
• Atomic layer 2, however, prints INCORRECTLY at 210 - Note that the issue here is not that the wrong temperature is being set it is that it is not setting a temperature at all, so it is just using the previous Hatchbox temperature.  It SHOULD be setting M104 S215 for the blue Atomic filament, but is NOT.
• Hatchbox then prints squares up to the color band correctly at 210
• Atomic blue color band then prints CORRECTLY at 215
• Hatchbox then prints correctly at 210 for the remainder of the print
• If I change around the order I can have instances where the first solid section up to the color band is all at the wrong temp.

Again not a huge issue if the filaments are close in temp, but if we have a Silk PLA that will not load and unload at 210 then it becomes a problem.

Attaching pics and the zipped project file and gcode.  Any ideas are appreciated.  

A couple of other items:

1. was going to mention the load/unload temp issue but just saw post by @anachronist that we are very excited to see if it works.  
2. As seen in the pics the temp legend still doesn't work for us (can't recall why that is)
3. Currently to solve this issue we have to manually change temps but even that isn't great as the temp will then be over-ridden by the slicer when get to different layers.  Not sure if there is a way to make manual temp changes "Stick".  

Thanks for any input