It appears that some strange preset is being applied as the master/"original image" (in new Aperturespeak) is reprocessed for a preview. What is a mystery is why you can't make adjustments such as recovery. If you view the master (M key) is it also the same? Does the metadata confirm that the master is a .PEF? Does an export to jpeg retain the poor image quality? If you create a new version from the master, is it similar? That would definitely tell you it is the processing that just happened is the culprit.
I wonder if the "boost" setting in RAW Fine Tuning is set low. (In 3.3.2 you need to go to the Add Adjustments dropdown to bring up the RAW Fine Tuning.) Everything I looked at as a sample has boost set to its maximum of 1.0. Setting it lower does darken the image. The preset for your camera(s) may be corrupted. You could use the gear menu to modify the preset. That does not explain your fourth paragraph, though.
Export a couple of masters and reimport them into a new library. Then compare the images using Preview on the master file and the image in Aperture. I believe they both would use the same RAW processing but no additional adjustments for Preview. This might help you isolate the issue. Just food for thought, wish I could be of more help.
I just upgraded to 10.8.1 and Aperture 3.3.2 with RAW 3.14.2. No problems with a library that has gone through several updates to Aperture. Most of the Pentax photos are .PEF from a K10 and now a K-5.
Al lot of good questions. I actually got ahold of Apple and got one of the Aperture team memvers after a few transfers and they saw the problem too. They had me send a lot of info to them, including some of my test files from my camera.
To answer (most of) your questions:
Yes, i really looks like its applying some preset, doesn't it? But it's not as far as I can tell. It does the same thing on my iMac as it does in my BacBook Pro, so the same thing happen on two different installs. Hitting M shows no difference. And yes, it does show in the info that it is a PEF file. I even tried today to get some shots on DNG just to see if it made a difference..it didn't.
if I send the file out to export as an original/master--it get's strange. If I use Preview to look at it, it looks like it did in Aperture after the "Processing" gets ahold of it. If I pull it in to Photoshop, it retains its RAW image look and has none of the darkening/shift issues I see in Aperture. So its my opinion it is something to do with Apple's Camera RAW processor.
Changing the RAW settings in the RAW brick in Aperture doesn't seem to make a difference either.
Good news is Apple sees the issue and is working on it. I head overseas for a Photoshop in three weeks. Really hope they can figure this out. I tried installing an older version of Apple Camera RAW, but it fails to do so indicating every time there is a newer version installed already. If I knew how to uninstall or erase it (don't even know where the files are) I'd give that a try. No luck locating them so far.
It appears that Camera RAW is in /system/Library/CoreServices. However, that gets into the treacherous world of sudo, so I did not go any further.
I may be way off on this. Just as you can softproof using a different color profile than the one for your display, I wonder if somehow a bad color profile is being applied as the images are displayed.
I believe Image Capture uses the same RAW processing. If a captured image direct from your camera looks OK, that may indicate the issue is not with the RAW processing.
This has been driving me crazy and is also ruining my work! I shoot with two separate Nikons only RAW and Apertoy still apply's this funky preset. Please help as this is no small problem. It is literally DESTROYING my work! I can't believe this is not affecting thousands unless they just don't notice it? Please, if anyone can help in this matter It would be much appreciated!