I'm not too familiar with Rek'Sai, but I use PoM almost every game. It works fine for most ults, but if the particle reaches you when your ult isn't actually counting down its CD - meaning the cast has completely finished and you see a timer for its CD - it has trouble. If your champ's ult uses charges with a tiny CD, like Teemo's, the CD refund is worthless. If it's recastable, like Pyke's, CD refunds during the recast window don't do anything. If it can be reactivated and only goes on CD after you do so, like Swain's, refunds don't count until after that reactivation. Basically, if your ult is not actually and fully on a traditional CD, the refund won't help.
When exactly does Rek'Sai's ult go on CD? And is it an ordinary, traditional CD? 7 seconds off sounds like it happened once with a rank 2 ult that had 10% CDR (rounded from 7.2). If she usually gets kills with her ult, I'd theorize that the CD doesn't actually start until after the attack, and, being close to the target when it dies, the particle gets to her too soon, before there's any CD to reduce, and that one time where it worked was for a random kill or assist you got when the ult was firmly on CD.