What focusing pattern are you using? Single point, expansion points, all points? (
I'm not sure which AF patterns 1DIV offers. I use 100-400 II with my 7DIIs, also with BBF and AI Servo much of the time, and find I get the most consistency when I use single point. Of course, that's more work keeping the point right on the subject. Sometimes I'll use expansion or small zone patterns, but mostly only when there's plain background and/or nothing too close behind or in front of the subject that might distract AF and cause it to lose tracking. I do see a bit less consistency, regardless, but use those patterns anyway when subjects are especially fast or moving erratically.
Some other ideas or possibilities...
Manual exposure should help AF speed, if anything. The camera not needing to meter and set exposure will usually make it faster.
Do you have a filter on the lens? I've seen filters cause issues. Do you use the lens hood regularly? I've seen those help AF performance at times.
My cameras (again, 7DII, not 1DIV) have menu settings that can be used to delay how quickly the camera jumps AF to another object, if I momentarily fail to keep the AF point right on target. It seems counter-intuitive, but I often set that to slightly "slower". It doesn't slow down AF or tracking, only effects how quickly the AF will move to a different target. It can be problematic if subjects are changing direction a lot, so other times I'll zero it out or even set it slightly faster.
Another setting I use prioritizes focus accuracy versus shutter release. Basically, it tells the camera whether I want the shutter to fire immediately or, if necessary, delay release until AF is achieved. There are two of these settings on my camera... one for "1st image" and the other for "2nd (and any subsequent) images in a continuous burst". If I recall correctly, this only functions in AI Servo.
Not sure if the 100-400mm is a "varifocal" or a "parfocal" zoom. I suspect it's partially varifocal (like most modern AF zooms). That being the case, AI Servo should immediately correct for changes in focal length while tracking a subject. But you might try locking the zoom in place sometime, see if you get better consistency that way (and it's nice the 100-400 II has that neat ring to quickly and easily lock or unlock the zoom).
Finally, I don't think you 1DIV even has AI Focus mode... but my 7DII do... and I avoid it like the proverbial plague!
You mention having "changed" some things... Anything else you didn't mention? Sometimes it's an unexpected item.
It might just be a matter of getting accustomed to the lens and it's focusing speed. While it's no slouch, I don't think it's quite as snappy focusing as f2.8 and faster primes and zooms, perhaps even a tiny bit slower than f4 primes & zooms I use. After all, it's an f5.6 lens at 400mm, f5 up to about 300mm if memory serves.
Oh, and one more thing I often do... whenever light allows, I stop the lens down a little. That just makes for slightly greater depth of field that might offset any slight amount of missed focus.
And, the other suggestions to run an MFA test on the lens are good ones.
Hope this helps! Let us know.
