2011 Mac Mini, 10.8.3, SSD - System CPU at constant 10%, frequent 0.5 sec cursor freezes

Question

Hi.  I have a Mid-2011 Mac Mini with 8GB of RAM. I have an SSD installed in it as the primary drive, along with another internal 2TB drive and an external USB 2TB drive for media. This machine is mostly used as a media server and player.  It's been running Mountain Lion since I bought it (refurb) last year.  I upgraded to 10.8.3 as soon as that came out, and was running for a while without any problems. This evening, though, I started to notice some problems.
The main issue is that the CPU (well, one core) seems to be constantly under load. Under Activity Monitor I'm watching the system load (but not user load) hover between about 8% and 12%, all of the time.  But looking at the program list, I don't see anything taking up more than about 2% of CPU, and that is taken up by Activity Monitor itself.
The annoying way that this manifests itself in the UI is that if I'm just randomly moving the cursor around in a circle, I can watch it periodically hang and freeze for about half of a second every 3-4 seconds or so. Meanwhile, everything else on the system also seems to freeze up for about half a second at the same time, which makes watching Netflix extremely irritating. (With Netflix the sound plays as normal, but the video freezes briefly every few seconds - I verified this in both Firefox and Chrome so I doubt it's a browser thing.)
I've already tried some troubleshooting steps myself. (None of this has worked yet.)
I saw a lot of messages in console about "mdworker deny mach-lookup com.apple.ls.boxd", which googling around for led me to this page; per the instructions there I booted into safe mode, waited a bit and rebooted, and now I don't see those messages any more. (I didn't mess with the sandbox.sb file, about which, really? Apple implemented this in Scheme or something?)  Just to be on the safe side, though, I disabled Spotlight indexing with sudo mdutil -a -i off.
I opened Disk Util and ran a verify on all three disks, no errors.  I found one or two permissions that needed repairing on the startup SSD and repaired them.  The problem persisted.  I also cleared out my caches with Maintenance while I was at it.
As a side note, even when I rebooted in safe mode, I was still seeing the same behavior (periodic half-second mouse freezes, system CPU averaging a constant 10% or so in Activity Monitor).
I also spent some time reading this other thread which looked like it had some very useful advice (unlike that poster, though, my Spotlight processes aren't crashing).  So I went ahead and followed Linc Davis's first set of instructions in that thread.  Here's what I've got for steps 1 and 2.
1. Activity monitor
Highest-CPU process is Activity Monitor at about 1-2% CPU
CPU: User 1%, system ~10%, idle ~90%
System memory: Page outs 0, swap used 0 bytes
Disk activity: Reads in/sec 0, Writes out/sec 0 (these infrequently spike up to about 40 or 50 max)
2. System log
I put up a gist for this here.  It's my last 50 messages or so, probably some are coming from the most recent reboot.  I can see the "IOHIDSystem cursor update overdue. Resending" messages which I presume are linked to my cursor freezes, but nothing else looks obviously suspicious to me.  The stuff about "menucracker" is down to MenuMeters; I uninstalled it and rebooted at one point just to check, but it didn't seem to make a difference so I reinstalled it.
As far as kexts go, the only one I had that wasn't Apple was SoundFlower. I actually need that one, I use it to stream files from Plex, but I went ahead and uninstalled it anyways, and it didn't make a difference.  My launchd lists start up sickbeard, sabnzbd, and plex, but I've manually quit all of those and the problem persists, so I highly douby any of them are to blame.
Any advice greatly appreciated.  Is there a better way that I can see what exactly is causing the high system CPU load, like can I list processes by number of kernel calls or something?  I did try top and ps but I didn't see anything obviously different from Activity Monitor in their output.

Answer 1

Nope, I don't have a "/Users/charon/Library/Mobile Documents" directory, let alone anything underneath it. Is that like an iCloud thing or something?  I tend to avoid the Apple-supplied services when I can (I don't use iTunes either unless I can help it).
As an update, as of about two days later this problem seems to have solved itself. Possibly sleeping and waking did something to it (though that seems unlikely given how many times I rebooted), or else there was just some long-*** kernel process that finally worked itself out.  But my system CPU is back down to normal and the cursor freezes are gone.
??? it is a mystery! ???