Looks like this is a runtime issue - since many mods add or update recipes, GDIW doesn't detect anything that loads after it.
In my case I'm running K2-SE, so if I set both of those as dependencies for it, then I am able to add productivity modules to flipped recipes again. (Even vanilla ones, since I'm guessing SE touches or re-adds them)
It did cause some issues with Recipe Book, so had to toss this in above line 67 of scripts/database/technology.lua
:
if recipe_data == nil then
goto continue
end
and then the label
::continue::
on what is now line 122