I've just been printed off a form for application of ShCM (long way off yet, I know) and I know that puppy group placings don't count towards your points, but does any knowledgeable person know the reason why this is?   

Because it is based on BOB, and thereby Group and BIS achievements.  Young stock have the JW to strive for.

thank you, I thought that was probably the case.

Of course if they allowed the puppy group places to count they would have an unfair advantage over the adults as they could get both points in puppy group and adult group if they are good enough to go BOB.