What does your union say?
The DES will contend that the fact that you are receiving incremental recognition for previous private work does not affect the fact that you have only started a state-funded incremental position after the 2004 deadline. Their argument will be that increments are awarded in a variety of circumstances, including non-teaching service, and there is no ipso facto pre-dating of start of service when an increment is granted.
I think you have a very good case and I would encourage you to press the union for support. One argument you can make is that you could have joined the state superannuation scheme while working privately for the secondary school (provided it - the school - is recognised by the DES). Thus the service you were giving is in no material way different to that you would have been providing had you been in service funded by the state. The key point here is that ALL teachers are employed by their schools; the state employs no teachers; the fact that the state funds most of the payment of most of them does not make the state the employer. Thus, you were in teaching employment pre-2004 and must be treated as such for superannuation purposes.
There may well be something written down in the regulations which they would rely on to deny you your pre-2004 rights. Even if this is the case, there would still be a compelling argument that such a regulation would be unfair.