The funny thing is that it was released uncensored first. The Shareware version was uncensored and got an MA15+ in Feb 1996. Unfortunately the Port Arthur massacre in April got the new right-wing government in hysterics about violent media.
By the time of it's full release in late May, it was apparently unsuitable for MA15+, but rather than making changes to the code, the distributor decided to force the game's in-built parental control mode on. The uncensored game was still on disc, and within days of its release pretty much every Australian was playing the uncensored version. I remember cracking it myself as a 12 year old -- it wasn't as sophisticated as the 'real' crack -- it forced adult mode ON, but the fact was anyone could modify duke3d.exe even without a hex editor -- opening duke3d.exe in WordPad or DOS Edit and changing the first ASCII 0 to a 1 was all it took.
Alarmed by the prevalence of the uncracked version (it was common to find it running uncensored in PC Gaming stores -- remember those?), the OFLC tried to recall the game but failed because they had been made aware the uncensored game was still on disc. At this point the distributor also submitted the unedited version.
The OFLC has never been known for their consistency -- but definitely not under the old pre-2003 code. Where an 'interactive movie' on DVD-Video could be given an unrestricted M, but the same title on PC CD-ROM went beyond MA15+ and had to be banned.