This is sometimes referred to the "thin wall" problem although some people say the "thin wall" problem is something else (where the wall is so thin that Cura prints *nothing*.
Anyway I recommend you get the beta as daid says. It's here:
http://software.ultimaker.com/Cura_closed_beta/
It seems to be working pretty well so I think it's relatively safe.
The other option is to lie about your nozzle thickness. So in your example the wall of the cylinder I suppose is 5mm-3mm/2? That leaves 1mm. So cura does a "perimeter" aka "wall" pass twice at .4mm each and that leaves .2mm to be filled. The new beta will fill that but cura won't. So instead tell Cura (13.03, not 13.05) that your nozzle thickness is .33mm or maybe even .3mm and it should make two perimeter passes and a fill pass. Look at the gcode graphically with cura before printing to make sure it does it right.
I assume you also have to set the wall thickness equal to the nozzle size. I haven't played with this much myself.
One would think lying about the nozzle size would cause other problems but people have said if the lie is small enough (from .4 to .3 is 25% change) then you will be okay.
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Daid 304
The new 13.05 beta improves this, as it fill fill up the gaps that are left empty in the old version.
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