Frameskipping and animations

I have couple of sprites set up with the animation system which involves switching the frames, but also updating the position of the gameobject. What I have noticed is that if the game stutters for any reason the animation system will skip the animation with an equal amount of frames. This is probably wanted in some situations, however in my case this stuttering happens sometimes when a new banner is loaded into the game and it will cause the animations to sometime skip so much that you cant even see that the sprite was even there before it walked past a door opening.

Which is a bit of a problem since you are supposed to shoot them when you see them.

Is there some way to disable this frameskipping (or at least limit it to X frames) or will I have to ditch using the animation system and doing it manually in the Update() function?