I run Veinminer 2.0.4 as well, and I don't know if it collides with this one or not, but I have noticed that Flash Forge doesn't work very well with any ores.
It does melt stuff, yes, but I get less drops than I should, as in I almost doesn't get any drops.
I also have Fortune 3 on my pick axes, and get the same result everytime. Here are some examples of mining veins or ores, both modded and not:

10 Iron Ore gave me 2 Iron Ingots
8 Iron Ore gave me 3 Iron Ingots
4 Iron Ore gave me 1 Iron Ingot
5 Gold Ore gave me 3 Gold Ingots
14 Gold Ore gave me 4 Gold Ingots
And so on in a similar fashion.

Modded stuff:
22 Nether Quartz Ores gave me 2-4 Quartz Glass (Better Nether)
Should give a ton of Quartz Glass, from 22 to almost a whole stack.
Cincinnasite Ore, no matter the vein size, just gave me zero Cincinnasite Ingots every single time.

And that is with Fortune 3. So yeah, something is off here.
It could be a collision with Veinminer, but it could also just be Flash Forge by itself.
I suggest checking both with and without the Veinminer mod, incase it only registers the first mined block or something.
Still doesn't explain the Cincinnasite thou (from Better Nether) which just doesn't drop anything at all with Flash Forge.

Right now I've chosed to only use Flash Forge on things like stone/cobblestone and similar stuff, instead of any ores, because then I mine 1 block and get 1 block as intended. But ores are busted for me right now.

If it is due to Veinminer, I'm sure something can be fixed somehow either on your end, or their end, or both. :)
Cheers!