Alpha channel from Quicktime into AE - broken?

This has been driving me nuts for some time. I am generating an animation w/alpha channel from my 3D software (FormZ.) It creates a proprietary .fan file containing the animation frames, which is then converted to Quicktime. I am using the animation codec, max quality, millions+ colors. When I import the QT file into Aftereffects, I get the alpha channel pop-up - so it apparently recognizes that something is there - but whether I choose straight or premultiplied, I just get black for the alpha channel with jaggy edges.
This is on OSX 10.5.5, QT 7.6, Adobe CS4. I have had the issue dating back a year or two, I had thought it was a bug that would be fixed by now - the same process used to work fine with older versions of AE and QT.
Now - the kicker - when I boot into Windows XP and do the QT (7.5.5) conversion there - then take it back to OSX for import into AE - THE ALPHA CHANNEL WORKS PERFECTLY.
I have talked with FormZ in the past, they recognize and have duplicated the problem. However, it is apparently a Quicktime issue so there is not much they can do about it.
This seems like a pretty fundamental issue that I can't believe it would go uncorrected for so long. Why would the Mac version behave differently from the Windows version? Am I completely missing something in the Mac QT? I have played with the various transparency settings under Movie Properties (QT Pro) - but all I get is a dithered mess when I try to change those settings and bring it into AE. I can't even find much discussion of it - I found a reference to Quicktime 7.1.5 breaking alpha channels, but nothing very specific.

Welcome to the discussions, austinpike.
Normally, QuickTime should work the same on both systems. However, there are some deep differences in how the OS's work that mean the code isn't fully transportable, so there's a chance some things might get missed, or changed, etc.
What you should do is go here.
http://www.apple.com/quicktime/feedback
And enter your details that you specified here. It could very well be that no one has reported this as an issue yet. I know I'd been perturbed by something in QuickTime I thought would just "get fixed" but a few versions after sending my bug, it was finally resolved. Hopefully, sending the feedback may put the wheels into motion to get it resolved for you.

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