GCode files that use the MMU don't use it when printing

[technopaw]

I have attached one of the many problematic gcode files. What happens is when I slice a file for MMU printing if I send the file via connect in Prusaslicer and immediately start printing it works as expected. If I get the gcode file to the printer any other way like exporting and uploading or uploading, then printing later it treats it as a non-MMU file. If I download the file from PrusaLink and open it in the Gcode viewer everything looks like how I would expect it to look. If I upload the file to an SD card and print from that using the printer menu or prusalink it works as expected.

Some additional details
Prusalink using the GPIO pins on a Pie zero w version 0.8.1
Printer is a MK3S firmware 3.14.0 and a MMU2S firmware 3.0.2

trasmission_components_0.2mm_PLA,PLA,PLA_MK3SMMU3_3h15m.gcode.zip