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Extruder 1 doesn't prime in 2 material mode

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I've got an Ultimaker 3, and I've been trying to use it with PLA in extruder 1 and PVA in number 2.

However, I've found that when trying to do a print that uses both nozzles, both extruders never extrude for the first few minutes. It's almost like the device forgets to wind forward the material to compensate for the retraction at the end of the last run.It's not that the cores are clogged because both work fine when they're the only core printing. The problem only occurs when I'm set to use both cores in the same print.

I've compensated for this by manually moving the material forwards before each print, but why does this happen?

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I have that issue on the Ultimaker 2+ and always do the Move Material function prior to a print to prime the print head.

On the Ultimaker 3, I have only had this happen once, even with the latest version of the firmware. I'd re-check the firmware for the latest. One the 5 prints I have done so far on the UM3 I have here, it's only done this once. (I manually moved material on each nozzle then did the print.)

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