This was driving me nuts on my Flexydually v2 using Cura 19.08. I couldn’t figure out why the objects weren’t printing all of the way. It turns out that in the medium quality profile for ABS/NinjaFlex, the profile is set to object_sink = 2mm, so the first 2mm won’t print. This setting is 0 in all of the other profiles…
Ah, I see Aleph is aware of it and fixed for the next release. https://forum.lulzbot.com/t/cura-not-merging-for-dual-extrusion/3412/1