I am trying to print this: http://www.thingiverse.com/thing:1596008, and got the top done fine, but when I preview the bottom part (3rd picture) the vents disappear in the preview. I tried flipping it 180 degrees just to see if it'd help, but no luck. Turning it on its side turn the vents into giant holes. I've tried changing the layer height, changing the raft/support settings, rotating on the z axis, nothing seems to help. I was using the Linux version but it was not the latest version so I tried the latest version on Windows with no luck.

I'm new to 3D printing but I've been having pretty good luck so far but this has me stumped. I tried replicatorg and a viewer shows the ports but when I tried printing the raft got messed up so I stopped the print. Any ideas?