There are times when the reward window will fail to show up and it happens mostly with Odin?Behemoth but Ive seen it happen with Steropes in Coerthas as well. I suggest next time you do one of those FATEs that you check your gil and/or seal count and if you should be getting silver check your inventory to see if despite the window not popping up you ARE receiving the rewards. Also are you a healing class? If so ensure you toss a few nukes at the boss since healing alone will not normally get you a reward.