I think I found the issue and it does look like it was fixed in CC-530. There are lines in this G-Code file with just F889.0 on them like this:
G1Z-2.00F304.8
F889.0
X166.99Y231.39
In CC-530 it is generating lines like this:
G1Z-2.00F304.8
X166.99Y231.39F889.0
Pretty sure the Duet Board would not like those.