I haven't had any issues using the reset config I got from canon - I have now reconfigured my own without touching the af settings and it worked fine last-night at another runway tracking black subjects at 1/250 f4 iso 10K <- this was not fun...)
I believe like you its a contrast issue. But the default configuration doesn't exhibit the same issues that I had with my tweaked config.
eg. single 60w equivalent cfl room light trying to track my gf face - the broken config wont lock on anything. The reset config locks on Her eye brows and eyes, under her nose and lips as if it was nothing.
The test with canon was well below -2ev (i could not see the other reps eyes yet the camera locked on as if it was nothing and focussed accurately) broken config just hunted - canon rep couldn't believe it.
As annoying as it is if you haven't tried it - i would recommend making a backup of your current config and send it to me, then testing out the config i got from canon - i'll pass your broken one to canon so they have a second point of reference.
I will also test out your finding tomorrow and get back you if i can replicate it