I thought about this after I wrote my reply, I have an older installer, 3.0.3 or so, that probably made a difference.
Try to install with Pacifist, they have a trail I think.
Will give Pacifist a go, thanks.
If this is happening repeatedly, then I would look for something else on the system that is causing the instability. Something must be different with your Mac and others who do not have the problem.
For reference... my latest iMac is a 2012 i7 iMac with a MX680, 32 GB DRAM, 768 GB SSD, 8 TB Pegasus Thunderbolt RAID array (4TB RAID 10). I still have the original Aperture 3 (on physical media) and it installed and has been running perfectly. I have used the machine with my ~400GB Aperture library on both the Pegasus, and the SSD. I am currently using it on the SSD. No instability problems... everything is instantly fast.
I hope that you get to the bottom of it.
BTW: When I moved to this new machine... I reinstalled everything from scratch, and abandoned about 1/2 of my applications that were not commonly used or redundant. I like lean clean installations whenever possible.
/Jim
This Mac is very similar to yours - except this has the 1TB Fusion and 16GB of memory instead. Of course it has been reformatted, and the OS installed from scratch (removed iMovie/Garageband/iPhoto and all that junk). I'm the same as you, a clean machine is my haven.
It's a fast machine, no instability issues whatsoever. I'm 110% certain this isn't a hardware issue. I'm not trying to toot my own horn, but I work in IT and deal with Macs on a daily basis.
Anyway, back to the issue. I tried a fresh install of the OS only, keeping the Users directory untouched. Issue still persists, which led me to assume it's something screwy in my user folder. Confirmed that by creating a test user. Aperture installs without a hitch.
Thanks again - I'll keep you updated.
----------
PS - here is the log from opening the mpkg, to closing.
21/04/13 5:03:16.191 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.192 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.194 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.196 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.198 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.199 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.201 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.202 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.203 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.203 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.204 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.206 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.208 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.210 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:16.212 PM CoreServicesUIAgent[1354]: Error: qtn_file_apply_to_path error: Read-only file system
21/04/13 5:03:17.436 PM Installer[1352]: This NSPersistentStoreCoordinator has no persistent stores. It cannot perform a save operation.
21/04/13 5:03:17.437 PM Installer[1352]: (
0 CoreFoundation 0x00007fff8ec5fb06 __exceptionPreprocess + 198
1 libobjc.A.dylib 0x00007fff92ab33f0 objc_exception_throw + 43
2 CoreData 0x00007fff90b2c889 -[NSPersistentStoreCoordinator executeRequest:withContext:error:] + 345
3 CoreData 0x00007fff90b55a98 -[NSManagedObjectContext save:] + 456
4 AELicensingPlugin 0x000000011481afa0 aelWriteLicenseFileLegacy + 1497
5 AELicensingPlugin 0x0000000114818d2d aelReadCurrentLicenseFile + 88
6 AELicensingPlugin 0x000000011480ff1c AELCheckLicenseFile + 64
7 AELicensingPlugin 0x0000000114810022 AELCheckLicenseFiles + 131
8 AELicensingPlugin 0x000000011480ddbb AELicensingPlugin + 7611
9 AELicensingPlugin 0x000000011480fb27 AELicensingPlugin + 15143
10 AELicensingPlugin 0x000000011480fad7 AELicensingPlugin + 15063
11 Installer 0x000000010c86988a Installer + 116874
12 Installer 0x000000010c85cfb5 Installer + 65461
13 Installer 0x000000010c866a2b Installer + 105003
14 AppKit 0x00007fff9348122f -[NSAlert didEndSheet:returnCode:contextInfo:] + 100
15 AppKit 0x00007fff9313cb46 -[NSApplication endSheet:returnCode:] + 267
16 AppKit 0x00007fff9347c986 -[NSAlert buttonPressed:] + 265
17 AppKit 0x00007fff9332f989 -[NSApplication sendAction:to:from:] + 342
18 AppKit 0x00007fff9332f7e7 -[NSControl sendAction:to:] + 85
19 AppKit 0x00007fff9332f71b -[NSCell _sendActionFrom:] + 138
20 AppKit 0x00007fff9332dc03 -[NSCell trackMouse:inRect

fView:untilMouseUp:] + 1855
21 AppKit 0x00007fff9332d451 -[NSButtonCell trackMouse:inRect

fView:untilMouseUp:] + 504
22 AppKit 0x00007fff9332cbcc -[NSControl mouseDown:] + 820
23 AppKit 0x00007fff9332453e -[NSWindow sendEvent:] + 6853
24 AppKit 0x00007fff93320674 -[NSApplication sendEvent:] + 5761
25 AppKit 0x00007fff9323624a -[NSApplication run] + 636
26 AppKit 0x00007fff931dac06 NSApplicationMain + 869
27 Installer 0x000000010c84e434 Installer + 5172
28 libdyld.dylib 0x00007fff8be1e7e1 start + 0
)
21/04/13 5:03:17.984 PM sandboxd[1358]: ([1219]) mdworker(1219) deny file-read-data /Volumes/Aperture Trial 3.1/ApertureTrial.mpkg/Contents/Plugins/AELicensingPlugin.bundle/Contents/Info.plist (pre-plugin fstype:hfs fsflag:480D000 flags:250000004C diag:0 uti:com.apple.generic-bundle plugin:internalPlainTextImporter - find suspect file using: sudo mdutil -t 1082346)
21/04/13 5:03:17.000 PM kernel[0]: Sandbox: sandboxd(1358) deny mach-lookup com.apple.coresymbolicationd