Do you think it may be possible that your sword is being blocked? If not, what is your framerate like when this happens? I'm Wondering if this may be performance related.
Sometimes their armor is really good at absorbing blows. It could be a case of that. Does the behavior change if you jetpack-attack them? I'm wondering if the attacks just aren't landing correctly, or they aren't doing the damage that they look like they should be doing. - I'm guessing this issue is intermittent? Again, a video would be really helpful. Programs like FRAPS, Plays.TV, Radeon ReLive, and Nvidia Shadow Play are some good options on that front.
-Cheers