Given your 12,000 images are 2.61 GB in total, they're about 228 kB each — is this right? and is this typical of your entire 280 GB of photos?
By default, Aperture makes previews and thumbnails to speed things up, based on the assumption that your images are quite large (e.g. 2+ MB) and loading + displaying them will take a long time.
For low resolution cameras, Aperture wastes quite a bit of space (relatively speaking)... but you can improve it somewhat...
Disable/shrink previews
If this size is typical of your entire library, you should probably disable the automatic creation of previews since they'll be pretty redundant for 228 kB images:
- In Aperture Preferences, go to the Previews tab and uncheck the box for automatic generation of previews for new projects
- In the library, click on Photos (at least in 3.x, in older versions you may need to make a search for all photos?), select all, click "Delete Preview".
If you really want previews, but want them lower quality/size, then change the settings in Preferences and then make sure you select all photos, right click and "Update Preview". You might need to delete them first if it says they're already up to date.
Not much you can do about thumbnails
According to this apple article, Aperture thumbnails are 1024x768 resolution JPGs, and I know of no way of disabling their creation. For low resolution images, this is obviously pretty silly/redundant, since the speed-up will be minimal. Other than complaining to Apple (that "fixed size thumbnails even for low resolution images is stupid"), I'm not sure what you can do here. :(
I have a library of 34,000 photos which has produced 22 GB of thumbnails, an average of 680 kB per thumbnail. For your 12,000 photos 4.9 GB of thumbnails its about 430 kB per thumbnail. This overhead doesn't really bother me, because my 12 megapixel JPG images are 2-5 MB each (and RAWs are more like 20 MB), but for a library of smaller (say 2 to 5 megapixel) images, the thumbnails aren't that much smaller than the masters...
Just a warning, that according to posts like this one, Aperture will slowly regenerate your thumbnails, so while you can delete them to save space, they'll slowly come back.
If you've only tried with your smaller photos from an older camera, and your newer one has bigger files, then you'll see a big improvement in the amount of space "wasted" in thumbnails once you put the larger photos in. 280 GB of 288 kB photos seems unlikely (1.3 million photos?!) so I'm guessing you've got some much larger images in there... in which case it might be okay in the long run...
Should be easy enough to calculate the Aperture thumbnail waste from the total number of images multiplied by about 500 kB per thumb.
Since more than one application is having issues, it's unlikely to be two bugs and more likely to be a system or hardware issue.
Before spending a lot of time, make a new user and see if that user has issues as well. You could have bad luck and lots of corruption in your user folder and this will let you know if the problem is with the apps/system/hardware or not.
Drive Genius might help to run more involved tests, but it might be cheaper to just buy a spare external drive and back things up. You can zero the drive and clear all bad blocks - give that hardware the best chance to work again. You will know soon after restoring your data on the newly erased and installed mac if the problem is resolved.
Good Luck!
Best Answer
I'm sure this could have a better solution, from someone with a deeper understanding of the OS underpinnings, however...
You don't need to start over to simply change the volume name, you can change it easily enough from the Finder, just click it twice [not double-click] just like you would with a file; or click then Return.
I often have issues if I clone a drive for experimenting with OS upgrades etc.
Everything just behaves better if I name the clone the same as the main drive & remove that original drive.