Yes this behaiviour is the same as in version 3.2.1. Looks like a bug to me.
I think this is suppose to happen: all diamond colors are unused document colors (the way I understand it). If you want one of the diamond colors to be part of your document, select the diamond color, open the color editor and then select "new named color" and it appears in the front of the palette as a square color.
In a way this is good behaiviour, when you export to .AI or .PDF only all square colors exported only, all diamond colors are ignored, it keeps the document quite clean.
Idea: Holding CTRL pressed on the keyboard while selecting a diamond color will make it a square color.
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