I have discovered that when I set the silkscreen "Break Shapes" to yes in the PCB Layer Types I get "filled in shapes" when printing the silkscreen layer. This occurs on footprints that have a PCB via placed in the silkscreen outline.
If I set the "Break Shapes" to no then the printing or outputting of the silkscreen layer does not fill in the component shape.
This issue will be fixed in the next patch, but for now you should be able to work around it like this:
Edit the footprint, select the shape that is causing problems, and do Properties. Check the Filled box, then uncheck the Hatched box, then uncheck Filled again. The presence of the hatched flag is what is causing the issues in plotting, even though it should be ignored because the filled flag is off.
If this is a big problem for you (maybe you have many footprints that would need altering) then please contact our support team by email (support@numberone.com) and we should be able to send you an interim fix.
I have been experiencing this issue since the original release of V21 , -despite a number of patches & updates. But I am pleased to advise that the latest patch (available ~1st June 2018) appears to be effective in resolving this bug. Thanks to Support team.