According to the Belgian constitution, each ofthe regional Parliaments are part of the federal parliament. Therefore they will have the right to complain about EU legislation if they think it contravenes subsidiarity. Naturally the Flemish and the Walloon parliament have not seen eye to eye about the precise details. But the debate in the Belgian federal Parliament about the Treaty was so curtailed by the political chaos in Belgium that this kink was not ironed out.
Thus what was deposited in Rome was not the ratified Treaty, but instead some rather bureacratic IOU saying that the Belgians have every intention of tratifying the Treaty.
Now I hear there is to be a legal challenge launched to clarify the situation.