I keep having something odd happen on tool change layers where it seems like it's got a clog or something causing it to partially miss a layer. It happens when I do infield first and it happens when I do walls first. It only occurs within layers that have tool changes. Has anybody seen this or know how to fix this?
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That actually looks like it might not be loading it far enough into the extruder. Are you doing a purge block before hand? And what do they look like? Another possibility is that you have a retract on tool change turned on and it's effecting it.