Robert posts good advice!
A few more things:
1) Try turning off "combing" which is in the expert menu. Combing forces travel moves "inside" the part wherever possible which is smart for lower layers but not good for the top and bottom layers. When combing is on, Cura turns off retraction for that move. So robert's "z-hop" suggestion might only work for these if z-hop is on. I'm not sure as this is a very new feature.
2) Look at the part in layer mode when you play with Cura settings. It might teach you something helpful.
3) Consider setting the "shell thickness" to 100mm. This will change the infill pattern and you might like the result better. Or conversely set "shell thickness" to 0mm which will give you *only* diagonal infill. I think you will like this less as the outer edge will be bumpy - but overall it might be an improvement to the top and bottom layers.
After experimenting - please let us know what you learned - along with possibly a picture!
Oh - one more thing - you might want to try "kisslicer". It's free and has a simple GUI just like Cura - although it has many more settings and is hard to figure them all out.
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IRobertI 521
This is caused by a travel move where the head is just moving to a new position. In the newest beta of cura which you can find here: http://software.ultimaker.com/Cura_closed_beta/
daid has added a "z-hop" feature that might help with this. It will lift the head slightly after doing a retraction and just before it moves to a new location. I haven't tested it out myself but it could be worth a look.
More info and reported bugs here: http://umforum.ultimaker.com/index.php?/topic/4487-bring-me-your-bugs-cura-1402-rc2-ready-for-testing/
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