Yep, that's exactly it. Here are some pictures.
So the cube is 20mm and at .1mm layers this makes it 200 layers. I have my bottom and top thickness set to .2mm which makes them the first and last two layers. When I don't have a raft enabled it works out just fine, you can see the top (last two) layers are solid.
So here I have the raft enabled and the raft is a total of .3mm making it 3 layers in this case. You can see the actual cube starts printing on layer 4.
This is the last layer of the print (200). As you can see the 3 layers of the raft have taken away from the top 3 layers of the cube and not just added 3 underneath resulting in the cube being unfinished. Do I just have to make the cube into a rectangle? I feel like that would be the wrong way to go about this, because what if you have some awkward shape that you can't just vertically extend?
If it helps, this is what I'm trying to print. And any help in terms of what setting to use that would be best to print would be awesome too. Thanks!