Factorissimo 3 deepcopy all belts in data update to create his connection for his belt but since you modify them in data final fix they no longer have the right speed
you need to add something like that in data final fix in you mods if factorissimo 3 is enabled :
and add factorissimo 3 in ? dependencies

local base_speed = 0.03125
local linked_belts = data.raw["linked-belt"]
for i,v in pairs(linked_belts) do
local speed = v.speed / base_speed
v.speed = base_speed * math.pow(2,speed-1)
end

I added the support for factorissimo 3 in the mod so everything should be fixed

Thanks!