Has nothing to do with time. 75 patch nerfed the amount of proofs you get down to 10. No idea why they felt such a rare commodity needed to be downsized, but it has been.
Not 100% true. When we did Wodjin and I had the Beacon, I spammed it on the boss to make sure I get it as soon as it was downed. Did the same for the other Wodjins, 1 I couldn't use since it was on cooldown, got only 10 for all 3. So beacon used twice on 2 wodjins, and 1 not used since beacon has a 1 hour cooldown.
Went on to do Spider Priestess, used beacon once (my last time), still got 10 Proof of Justice. Went to turn in for my 60, no beacon in inventory (or raid) and we got 15 Proof of Justices for the last 2 Spiders. (Yes, 15.)
Not sure if its because a Beacon of Courage is in the raid, or time/level of raid, but 15 Proofs can still be obtained after this patch. Just not exactly sure what makes the loot go from 15--->10.