Actually - no, I wasn't misreading things there, and that's not what I was asking.
Firstly, both contracts did NOT count against the cap, only the second 'larger' one counted for the cap breach. Had the NRL just looked at the 'legal' ones then they would've been fine (why cheat if you can't even get that right). The players weren't getting paid 2 contractual amounts, just one.
example: sign for $650k and lodge a $400k contract at NRL HQ. Player isn't getting $1050k - and the amount that they are over the cap for that contract is $250k (not $650k).
The question I'm asking is: HAS the NRL come out and said that the 'lodged' contracts are the binding ones going forward? Ie, the players 'fake' $650k contract will be thrown in the bin and they will get paid the $400k one. This is a problem for the Storm still since they also arranged 3rd party deals (eg $100k for this hypothetical player) and that amount puts them over the cap and must be counted now. But it'd be a damn shame if they were only over by that amount rather than the full whack.