Figures look completely different in Illustrator (exported as .eps)

On the right side of the image you see my figure as it should look like (rendered using painters). However, no matter how I try to import it to Illustrator (I tried save as.. / and export_fig from file exchange, trying .eps or .pdf ...), it always looks weird (left side is in Illustrator): the line thickness is different, even though I defined it in the code (I can work around this by just setting it much thinner in the original figure, but its an unreliable trial and error for every figure...), the worse problem is that the white lines that I was drawing above the axis are not placed correctly anymore and no matter what I try in the code it doesn't get better...

(strangely, the white lines also disappear when I use zbuffer as renderer, maybe there is another way to achieve this effect of multiple spaced y axis?)

[Daniel Shub]

As Jan says in his answer, there is a lot going on here beyond the section you circled. Please edit the question with some minimal code that will allow us to recreate the problem. Presumably the circled problem doesn't require the colored lines or the grey bars. We also probably need your OS and illustrator version and how you are exporting the images.

Answer 1

[Jan]

You do neither explain explicitly how you have created the diagrams nore how you have exported them. "...the white lines I was drawing above..." could mean a variety of things. Posting the corresponding commands would be important to understand the problem.

[Felix]

for example this would make part from 0 to 1 of the y axis disappear (with painters at least...):

xlim([-5 640])

line([-5 -5],[0 1],'Color','w')