Alright. Here's the deal: I measured the ERD using 2 spokes w/nipples installed,and nicks cut into each at 180mm from the bottom of the nipple head slot.
I inserted from opposing spoke holes and measured the distance between nicks using my spoke length gauge to both align the spokes and measure the distance.
This is pretty close to the method which Wheelcalg describes in their help section.
Total distance is 600mm, or 4mm more than the specs found online in several places including calculators which have the Dyads in their databases.
So, I guess I have egg on my face on this one.
However........ (read "In my defense")
I have built many,many wheels using this program, including wheels using Dyad rims. I have always used the manufacturers' published dimensions and never had this issue.
Never.
I looked at the previously built Dyad wheels in my shop, and they have NO spoke threads exposed, using the same Sapim spokes and nipples.
I reviewed the data from those builds and I used Velocity's published 596mm dimension. Had I used 600mm, the spokes would have been too long.

So, what do I do in the future **********?

Most wheels I build with spokes calculated by this program pretty much allow the spoke ends to be evened up at the base of the slots before final tensioning is applied.
That is one method I like to use to establish a baseline for tensioning. It usually proves to be pretty close as a starting point.

FWIW, I threaded a sopke through the spoke heads on the wheel that I have built with the spokes that are too short, and the spoke threads in 6 turns +/- before contacting the end of the installed spoke. The wheels were not brought to final tension, and I would estimate that there needs to be 1 turn +/- to bring then to final tension. From what I can see, that means that the ends of the spoke would not quite reach the transition between spoke barrel and head. Although it is a front wheel and I could probably "get away with it," I will order new spokes and relace. I can use the NDS spokes from the previous calculation on the DS of the rear wheel, so I only need 54 spokes + a few spares.
The program calculates 3mm longer, Is that safe, or, should I allow for the rim to shrink under tension?

BTW, the program from Professional Wheel Builder shows a schematic of the various dimensions, and the box for entering the ERD clearly shows this as the inside of the spoke hole. I guess they adjust their calculated lengths to add for nipple head height??