Hmmm I switched back to ctra 4 days ago - because either XRS or PerfectRaid cause very small but annoying hickups when many debuffs are occuring (like the lava-packs in mc or the spider-packs in Naxx).
The new xrs? Maybe you have defined too many buff buttons?
I'm sorry if this answered somewhere but I looked thru the thread and didn't see it, but I might've missed it since I'm damn tired atm.. ;) Anyway, I tried adding Prayer of Fortitude and Prayer of Spirit buffbars, and when I do it just shows up as noone missing the buff even tho noone in the raid has spirit/fortitude. The predefined single-target versions works just fine tho along with everything else
The only thing I can think of is that you didn't set the classes/groups for the buff buttons. Right click the button and select all classes, then it should work.