biglongdarren,
Just to be sure there are no other factors causing this, other than brood box size, are the configurations all the same - same floors amount of ventiation, sizes of colony, health, and maybe more?
What is the present weights changes? Are they simply using fondant as an easy alternative to uncapping? For instance is the box full of ivy honey?
Sugar is still cheaper than fondant - by a wide margin if not purchasing a lot. Full frames going into winter means better hive insulation. By all means feed fondant in the autumn, but remember they may only be able to take it down and store it in the daytime - as opposed to sugar syrup, which can be procesed at any time (dependent on temperature, of course).
How much fondant have the 'other two used? If it is naff all then ten times naff all is still not a lot, if you see what I mean.
The 'proof of the pudding', in this case, will be development in springtime. Keep this in mind when you find loads of bees and little brood because of a shortage of laying space (it happens more often than you think!). When one gives it some thought, perhaps that is one reason why shook swarms in spring appear to get ahead, so well. The alternative thought, particularly for beginners or those with few colonies, is better to be alive in the spring than dead with adequate stores still in the hive.
I rather tend towards the fact that the bees would need to cluster and feed in nature, so they can cluster and feed in a hive. Framed hives are not strictly comparable in every way to a natural comb built by the bees, but not that far away.
Apart from that I am with Rosti, really. And maybe they have moved upwards and are now directly beneath the fondant and are staying warm (or it's too cold to move to the full frames of stores?).
Regards, RAB