I recently started having focus issues with my most-frequently used lens, the Canon EF 24-70mm f/2.8L. It would often rear-focus a lot, despite using only the centre focus point and single-shot focus mode. This rear-focusing behaviour didn't occur all the time, and it seemed to occur more frequently at wider focal lengths.
There was also some in/out movement in the lens barrel that I previously hadn't noticed, and I suspected that this movement was related to the focus issues.

Here's an example photo, showing the bad rear focussing behaviour. The photo was taken using the centre focus point only, and single-shot focus, focusing on the face of my oldest son.

While the rear-focusing isn't particularly obvious in the scaled-down photo above, the 100% crop below shows it much more clearly.

The 100% crop shows that the lens has badly rear-focused, with the kids' faces out-of-focus, and the rigging and deckhouse in the background is in focus.
I remembered reading some interesting focus test results on the Canon 24-70mm lens some time ago, and found the lensrentals.com blog post (scroll down to the section titled "The 24-70 mystery").
In that post, lensrentals.com explain how they have noticed that the focus accuracy of the 24-70mm lens degrades over time, due to plastic collars in the barrel tracking mechanism wearing and falling apart.
The symptoms matched what I was seeing, and worn / broken / missing plastic collars also explained the movement I was experiencing in the barrel of my lens.
My 24-70mm lens was purchased new, about 3.5 years ago, so it was no longer covered by Canon's warranty. I dropped my lens off at my local Canon retailer, and it was sent to Canon for investigation.
It was about 4 weeks before I got the lens back - and as expected, the plastic collars were the issue. At AUD$485, it wasn't cheap, but because I use the 24-70mm lens so much, I figured it was worthwhile repairing (unlike my earlier experiences with the cheaper 17-85mm lens, which I repaired myself).
These repairs have also eliminated the movement in the lens barrel.
Testing with my newly repaired 24-70mm lens confirms that the focus is now operating correctly under a variety of conditions. Who knows - maybe the focus performance will be better than when new (I've previously written that I wasn't overly happy the performance of my 24-70mm lens).
Hopefully Canon have modified the collars and internal construction to address this issue in the recently-released and updated 24-70mm f/2.8L II lens.
Glad to hear you got the mystery solved. Lens repairs (or any repairs) from Canon are never cheap.
I'm interested in the 24-70 f/2.8L II - I've been waiting for it and hoped it would have IS (the reason I originally bought the 24-105 f/4L IS). The price of the new version is a little dear.