It can happen when you're somehow obstructed from doing the full damage in the animation I think. I don't use that headshot->melee often so I haven't had this problem yet but with CdG plenty of times. Occasionally a fireman, Bloodshot or BSAA soldier will survive one if you don't hit it correctly. Sometimes when you're too fast, you can even completely miss the target with the CdG animation resulting in zero damage dealt. If you've countered a lot, you'll know that sometimes, you can one hit kill certain zombies if you hit it frontally, stun it if you hit it from the side. In Leon-1, there is one lone zombie when you get to the turnstiles after the spitters' section underground. If you stealth attack it with Leon, you'll do that move (forgot its name) and hit the turnstiles and the zombie survives, if you stealth attack it with Helena, you'll do her sweep/elbow drop and it dies because you're not being obstructed. I'm almost certain there is no individual difference in stealth attack.
Enemies get damaged by melee attacks even if they're not the current taget. Most enemies in UC do have higher health compared to other zombie maps and this is obvious when you're trying to counter them. I don't know which skill you're using but not getting a kill from headshot>melee in UC is pretty normal unless they've patched it recently.