Okay, so the results are in.
I left the bios battery out and the system unplugged while I was at work for roughly 9 hours.
First and foremost I ran the utility F5BJR suggested after only setting AHCI, and my latency was a smooth 40-50µs, no abnormal spikes whatsoever.
Next I restarted, loaded optimized bios defaults and tested my three memory modules, first by letting it select the timings automatically, then after a second reboot I tried set the timings manually according to the CL9 SPD. For the Corsair XMS3, I also configured it a third time, this time using the XMP set to Profile1, and manually set the DRAM voltage to 1.50 to stay within the spec of the board. In all cases, the timings in the bios status screen showed up as 9-9-9-24 and a command rate of 1, although it even showed up as that when I had the XMP set, so I'm not sure how accurately the bios was reporting it.
For every setting I tried, after booting into windows (I tried with my fresh install on my other drive a couple of times for good measure), the timings were reported as 6-6-6-20 and a command rate of 2T, even for the Corsair XMS3 when it was using the XMP Profile1. The memory frequency, however, was at all times correctly reported as 666, and 800 for the Corsair when it was set to XMP.
Edit: Okay, so I decided to stick both 4GB sticks of my dual channel kit of G.Skill in as a final test, and when I booted it up, the timings were 9-9-9-24 1T as they're supposed to be. Now my XMS3 is also part of a dual-channel kit, but the unnamed Corsair ram isn't, and still showed up as 6-6-6-20 2T, so it seems to be specific to when the memory is configured in single-channel.
Double edit: I found this thread, which seems to be very much like my problem
http://forum.giga-byte.co.uk/index.php?topic=5552.0 ! I'm going to try using memory channel A and see if it makes a difference like it did for that guy.
Triple edit: Just as I suspected, putting the stick in channel A causes the timings to show up as 9-9-9-24 in both CPU-Z and Speccy. Now whether this is a mere cosmetic issue or something more serious is the question. Interestingly, I actually had a hard lockup after around 5 minutes of having both of my G.Skill modules in dual channel mode, but still haven't crashed running with single modules.