I've had a similar issue with Contagion. It just decides there is water/blood where there isn't sometimes. It can also REALLY screw over your elven friends, as well.

The only way I see Soul Shackles being worth it (Since it doesn't actually TRANSFER the damage, it just deals the same amount you take with the target) is if it pierces Magical Armor. Why?
1) The only really viable character to have this on would be a tank/warrior. Neither of these have any decent ways to break Magic Armor.
2) Most targets you want to kill quickly have a fair amount of Magical Armor to prevent them from being stunned and ignored. But this also shuts down this ability.
+) Possible solutions? Make Soul Shackle similar to Chloroform. Have it do damage ONLY to Magical Armor, THEN apply the check.