Sugarcreek16: This thread is actually well over a year old... are you asking a question about your own dog, or the original poster's dog?
Either way, no it is not normal for a boxer to have green eyes at any stage of life. In fact, it is most unlikely that any dog or puppy with eyes that colour is a purebred boxer.
White boxers may sometimes have clear blue eyes - but that is caused by lack of pigmentation. And pigment dilution may also cause some boxers to have light brown eyes (this is not desirable though - eyes should be dark brown). Likewise, some puppies have blue-ish brown eyes that will become brown as they get older (but the eyes are brown with a blue-ish tinge in the first place, not clear blue).
But if you've got a puppy that has greenish/yellow eyes, then it is very unlikely that it is a purebred boxer. Papers prove nothing - except that the breeder said the dogs on the papers were the parents of the puppy in question. Registration is purely an honour system, and some "breeders" lie.
If you're in doubt, and want some opinions, you could upload some pictures.