OK, I found a workaround. First use the plot2svg command on File Exchange, then use inkscape to convert to PDF:
plot(0,0,'ob')
plot2svg('uu.svg',gcf)
system(['"E:\Program Files (x86)\Inkscape\inkscape.exe" ' pwd '\' 'uu.svg'...
' --export-pdf="' pwd '\' 'uu.pdf"'])
delete('uu.svg')
This isn't super satisfying, but at least circles can be generated for pdf's.
If anyone has a more native solution to this problem, please let me know.

