I think the full version has an evolving rhythm which is really interesting and gives it an authentic feel to the overall sound, whereas the short version is almost like it doesn’t have enough time to shine and is easily dismissed as it doesn’t have the same level of impact as many other logo tracks of this kind already on AJ.
Maybe if the same reviewer had heard the short version along with the long version, then it may well have been accepted, but it is likely that they were reviewed separately, and without the context of the longer version, I think much of the magic is lost.
It is worth remembering that the reviewers are humans making subjective judgements on creative works made largely by other humans. Whilst their decisions are not arbitrary, they are not rigid like a machine either. Here is a really interesting thread which explains the review system really well and I think it might help explain why this has happened to you.