looks pretty good - try printing a little hotter.
Also measure the diameter of the extruded filament.
If you don't have digital calipers - get some: https://www.amazon.com/Tacklife-DC01...gital+calipers
with a 0.4mm nozzle filament can extrude anywhere from 0.4 on up to 0.6.
It's important that the slicer knows what diameter the filament extrudes at.
It might simply be that the mh filament needs to be extruded a bit hotter.
Probably better quality that the free stuff so might not expand as much when heated. Also the clear filament does tend to behave quite differently to the coloured filament. In fact every colour of filament behaves slightly differently, due to the colourants.
For example - not only is yellow the hardest filament to make, it's one the hardest to get decent prints with.

Your slicer should have a control panel that lets you move the head around and extrude, retract etc.
https://community.ultimaker.com/topi...ntrol-in-cura/
Or maybe not !
I knew I was right to dislike cura :-)
Doesn't look like slic3r does it either, by itself.
Your best bet is probably pronterface: http://www.pronterface.com/
A pronterface & slic3r combo will give you a lot more control all round and should be easier than cura to use as well. :-)