If we have this level of disagreement, then we have ambiguity that needs to be corrected.
If someone said "We can't start the class yet! All the pupils aren't present," then in that context, you would infer that some are there, but some are still missing.
Even without this context, that would actually be my first interpretation.
So, much as it pains me to ever disagree with LRR, it's perhaps a BrE/AmE thing, or perhaps simply hard to tell.