New Unity 4.5 Transform Organization Bug?

The current set up for our project has to have consistent transform organization. Which, 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 this before I hit play:

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

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After I hit play, and even persisting after I hit stop, it looks like this:

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

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

Again, this appears to be completely random and started immediately after updating to v4.5.

Why is this happening? How can we fix it?

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Thanks for your help!

Howey