As an update, because I haven't posted in this thread in a bit, Cura is still giving me this same issue with some prints, no matter how many times I reprint or re-slice in Cura.
Example: https://i.redd.it/ud40tsspo7921.png (Excuse the not-perfectly-tuned Slic3r settings, it's just there as a control to show that my printer can do this with other slicers just fine)
It's always at a set location for every layer. I have M400 as a start gcode command, so it's not a printer buffer issue.