Bug with items stored both as AAC and lossless in same library

I have an itunes library of 16000 tracks spread across 2 x 250 GB drives encoded as apple lossless.
I have also converted all the tracks to AAC, for ipod and airtunes use, and these tracks live on a 3rd drive
I therefore have 16000 tracks in Apple lossless and 16000 identical titles in AAC in the same iTuneslibrary.
Sometimes when clicking on an AAC title it instantly changes its kind to apple lossless and links to the apple lossless version of the file. When the library updates I often have thousands of AAC tracks changing to the apple lossless references.
I can fix this by emptying the entire library and reimporting all the tracks using add to library. I just did this and again had 16000 of each file type.
I then upgraded iTunes to 7.02 and upon lainch iTunes went into an automatic updating library routine.
After it had finished I had 22000 Apple lossless tracks (i.e 8000 were new duplicate entries) and 8000 AAC tracks
I had previoualy backed up the library after addinf all the files to an empty library so Ieplaced the library and.xml files and reopened itunes.
Itunes openend with the correct number of files, but then immediately went into its updating library routine and again lost track of what should have been an AAC file and what should have been apple lossless
The only thing I can think of is that the database is getting confused because the file extension for apple lossless and AAC is .m4a
I have tried to replicate the problem using a small library on another computer, but can only conclude that the bug only affects large libraries, or libraries spread across multiple disks.
Any help gratefully recieved as having spent 6 months ripping my CD library this problem is driving me mad.
Best Regards
Mic

When you say they change to lossless, does iTunes
simply think they are lossless or does it actually
convert them to lossless (which would take a minute
or so for each song)?
No the AAC entries change to kind=lossless and they then reference the lossless version of the file. The files themselves remain unchanged, deleting the entire library and then adding the folders to the library restores the original setup
A variation on this behaviour is that merely clicking on an AAC file will immediately change the kind of that file to lossless and the library entry will point to the lossless file. I can't reliably replicate this one, it just happens from time to time.

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Author:   [email protected]
Date:     2009-08-13 15:53:43 -0700 (Thu, 13 Aug 2009)
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Fixes bug with shader-transition effects (AnimateTransitionShader, Wipe, and CrossFade) when acting on targets that either have filters or are inside a hierarchy with filters. Fix was to capture the bitmap snapshot of the target without any of its own filters applied and to then use the ShaderFilter in conjunction with the target's filters during the animation.
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Bug with items stored both as AAC and lossless in same library

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