All RAW files suddenly said to need reprocessing

Question

I am running Aperture 3.0.3 with OS 10.6.4 so everything is as up-to-date as can be. I upgraded from Aperture 2 within a week of Aperture 3 being released and all my RAW files were updated in the process. Since then, I have added several thousand more pictures directly into whatever the latest version of Aperture was at that time. My RAW files are all from a Nikon D40.
The last time I used Aperture (about a week ago) everything was normal, but today the program suddenly tells me this about all my RAW files: "This photo was adjusted using an earlier version of Apple's RAW processing"
Obviously this should be impossible for the several thousand of pictures that have only existed within Aperture 3 as they would have been automatically processed using the latest version. However, if I filter pictures by which RAW processor was used for decoding, every RAW file except the 6 new files I just imported to check (they correctly show RAW Decoding 3.0) shows that it was decoded with RAW Decoding 2.0.
If I push the reprocess button, my photos change slightly, becoming a little brighter, a little warmer, with a touch more saturation. I exported some JPEGs to compare to pictures I have outside Aperture and there is a definite (but subtle) change after reprocessing compared to my original edits done in Aperture 3. All quickbrush adjustments are available for all RAW files as well, which I thought was only possible if the file was updated to the latest processing...but I'm not sure about that.
I restored my library from a vault (updated about 1 week ago, unsure if before/after this issue began) and I get the same message. The only change I've made recently has been installing the Camera RAW update that came about in the past few weeks. Is it possible that made this suddenly start happening?
Of course I want to have the latest RAW decoding for my files, but I'm concerned that pictures I edited and exported months ago appear to have a different version of RAW processing than Aperture now wants to give my files. Anyone with a clue of what's going on or what I can do to troubleshoot this issue.

Answer 1

Aperture user since v1.0. Nikon D70.
You're not alone. This message has recently appeared on my entire library of D70 RAW images, excluding my two most recent imports.
At the same time, many precious, carefully hand tweaked images have taken on a very pronounced dark green colour cast (which renders them as completely useless). It seems that the more carefully the file had been tweaked, the more likely it was to have been affected by the dark green cast. I am extremely disappointed by this.
FWIW. Depending on their vintage my images may have been originally processed in RAW Decode v1, v1.1, v2 or v3. All images were reprocessed in RAW Decode v3 when Aperture 3 was originally released.
Reprocessing the images using RAW Decode Version 3 removes this colour cast but also creates images of a different pixel size! Previously they were 3024px by 1998px; after reprocessing they are 3008px by 2000px. This is the size that Adobe's and Nikon's own RAW processors produce, so the previous dimensions must be seen as Apple's mistake (I reported it as such when Aperture 1 was first released, so I suppose we should be glad that they've gotten round to fixing it).
This change in pixel dimension is covered in support.apple.com/kb/TS3114 which says that the change occurs after upgrading to Digital Camera RAW Compatibility Update 3.3. Of course, the release notes for Digital Camera RAW Compatibility Update 3.3 made no mention of this. And Apple seem to be playing the whole affair with their customary stone wall.