Absolutely stunning images!
Lets try and sort this out, between AF settings vs. faulty equipment.
1) Were you using AI Servo or One Shot Mode?
2) If you were using AI Servo, then what is the tracking sensitivity set too?
3) Were you using Single AF Point or Single Spot AF point?
4) If you use regular Single point AF, then do you have AF expansion on or off?
5) Do you use half shutter-button press to focus or AF-On back button?
6) Were your red AF points on the subject or on the wall when viewed on your computer?
7) If the red points were on your subject, were they on a low contrast solid color, or on a higher contrast edge, or transition area?