two minor problems

I'm printing a pipette that I found on thingiverse but I'm having different issues on each of the components.
I printed the body of the pipette just fine.

Some of the other parts gets annoying.
I have the raft set up in matter control and the raft is printed for one componant but for another component of the pipette, the darn 3d printer doesn't even try to print it. It skips the raft making step and then obviously the thing doesn't stick at all.
The component where the raft refuses to print is a vertical tube with a smaller print diameter..... its just very tall and it wont print the raft for some reason.

Also another extremely annoying problem is the bed leveling. I use cura to do bed leveling for me, and its great and all, but then I switch back to matter control for the actual print and SOMETIMES it decides to lift the z axis before printing and totally ruins my previous bed leveling efforts and ruins the print.