I've been having the same issue, it happens every once in a while, usually during dailies. SB:SS applies Agony and Corruption but no UA. I am hit capped however a portion of my Hit is from Expertise, I can't imagine that would effect anything but just thought I throw it in there.
It is better to have raided and wiped, then to never have raided at all.
I've been having my Agony failing to apply when I SB>SS but I make do.
It has been a known issue since mid cataclysm that if you soulswap onto a target that is going beyond max range, like if you're on your flying mount flying past and stuffs, then all, some or none of the dots can be applied, depending on latency and distance.
There's missing, shown in combat log and stuff, and then there's <nothing>. If you encounter weird mechanics like this, try to repeat it and check the combat log, if the first one got flooded.