New Unity 4.5 Transform Organization Bug?

The current set up for our project has to have consistent transform organization. W$$anonymous$$ch, should theoretically work even better with the new way Unity 4.5 organizes transforms (However you line them up in the list, is how they stay). Unfortunately, for some reason when I run the game, it reorganizes the transform list and dumps transforms at the top of the list, to the bottom. And it appears to be completely random.

It looks like t$$anonymous$$s before I $$anonymous$$t play:

00Transform, 01Transform, 02Transform, ...etc...

.

After I $$anonymous$$t play, and even persisting after I $$anonymous$$t stop, it looks like t$$anonymous$$s:

01Transform, 02Transform, ...etc... , 00Transform

.

Usually it dumps the first transform to the bottom, but sometimes it dumps multiple down to the bottom.

Again, t$$anonymous$$s appears to be completely random and started immediately after updating to v4.5.

Why is t$$anonymous$$s happening? How can we fix it?

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Thanks for your help!

Howey