Strewf,
If you complete a CASA class 1 medical (you can book in for one any time you choose) and fail the Isihara test, as I suspect you already have, you can go straight ahead an ask to do the practical lantern test. If passed, this will give you a class 1 medical. Once you have this, I can't see why you cannot produce this to Airservices and gain an ATC licence at the completion of training. ATC licence applicant onlt require a class 4 medical as far as I'm aware and a class 1 would cover you for this.
I personnally, failed the Isihara (miserably), then the Farnsworth (FALANT) and finally passed the "Practical Lantern test" which was a case of sitting in a dark room facing a mirror, whilst identifying a series of either white or red light combinations. I am now a Boeing captain in a major airline as a result.
Dr Arthur Pape in Geelong is a very good person to speak to if you have any problems or otherwise feel free to PM or email me.
Good luck.
Yon Garde.