[Prusaslicer] prints are smushed after first layer along the z-axis, single color prints with same settings print perfectly

But when I'm printing with multicolor, after the first layer, it's like the z axis doesn't lift up anymore, and the nozzle scrapes the print and no filament can really extrude because the distance between the nozzle and bed is basically 0. BUT if I change the print to single color (with same exact settings, minus wipe tower) , it prints just fine.

Is this a bug in prusa? Any experience with this? My tool change code does not touch the z axis at all but I'll post it anyways, I will also post my project .3mf.

After the print goes for half an hour or so, I'll look at it, and the printer itself says the layer is 3-4mm's., BUT the nozzle is still right against the bed, scraping the print and not extruding anything. This only happens with multicolor prints.

; 3D CLIPPY TOOL CHANGE CODE ; Auto generated 3D Chameleon Tool Change GCode for PrusaSlicer - Chameleon As Extruder ; retract now to the cutting point to avoid ooze G0 E-55 F10000 ; go to holding position to unload the stock extruder G0 X220 Y210.5 F4000 G91 ; set motions to relative for the button presses ; - 3D Chameleon Tool T{next_extruder} - ; unload extruder {previous_extruder} ; begin switch from extruder {previous_extruder} to extruder #{next_extruder} ; M117 Unloading Tool T[previous_extruder] M92 X8; set x steps per mm to a small value (very high torque) G92 X0 ; set to 0 so we have a lot of room to travel M117 Cutting ; cut off the filament tip G0 X310 F10000 ; quickly cut the filament strings off G0 X-310 F10000 ; ok... go back to normal position M117 Restoring M92 X80; restore x steps per mm to normal value G92 X220 ; restore original position M117 pulling and homing G0 E-2 F4000 ; pull filament off blade (this will pull off the tip if it didn't cut all the way through) G0 Y-10 F4000; move away from clips ;G28 X R0; home the x axis to reset the position; HOMING DISABLES MESH LEVELING!!! replacing with next line G90 ; switch to absolute mode G0 X0 F4000 ; move X gantry all the way to the left G91 ; switch back to relative mode G0 Y10 F4000 ; push off tip into ptfe tube G0 E5 F10000 G0 E-7 F10000 M117 retracting ; retract it back out of the extruder G0 E-100 F6000 G0 E-58 F6000 ; ok - out of extruder - press button to remove it all the way ; load extruder #{next_extruder} M117 Loading Tool T{next_extruder} ; always reset to extruder 0; why? Lets just use an if statement again {if next_extruder==0} G0 Y3 F4000 G4 P500 G0 Y-3 G4 S2 {endif} ; press the button for each extruder (1,2,3) {if next_extruder==1} G0 Y3 F4000 G4 P900 G0 Y-3 G4 S2 {endif} {if next_extruder==2} G0 Y3 F4000 G4 P1400 G0 Y-3 G4 S2 {endif} {if next_extruder==3} G0 Y3 F4000 G4 P1900 G0 Y-3 G4 S2 {endif} ; - 3DC Process Tool {next_extruder} - G90 M83 ; return to position top middle G0 X105 Y210.5 F6000 G0 E100 F6000 G0 E100 F6000 G0 E27 F6000 ; one at a time was 19 G92 E0 M117 3D Chameleon Tool T{next_extruder}