I think ISTQB is more accepted as courses and certifications are being run here down under.
ISEB is also well recognised but seems to be slowly phasing out to be replaced by ISTQB.
This does not mean that a CSQE certification is not suitable. I am sure many companies would know the value of such certification.
I belive (from what I see in job adverts and talking to companies HR deps) that the ISTQB is more recognised on an international level (like for ex. here in Europe). I would not know about Australia, but if you plan to work abroad, then the ISTQB might be the better choice right now.