This happens to me sometimes when the material is in that ready position, a few cm back from the head. It doesn't reprime the print cores when it is in that position, so any ooze during cooldown or heating up is lost material volume that is unaccounted for and results in an empty head at the start of the print. Bizarrely, on the first layer, it prints the prime tower after the part, so you end up with missing extrusions. I just enable the prime blobs to make sure I've got the heads primed and the problem is taken care of.
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gr5 2,224
I have an S5 but I don't have the material station so I'm not certain but this sounds familiar from quite a while back (maybe a year) when a new firmware version fixed this or something similar. So make sure your firmware is at least no more than a year old.
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