The reason that happens is fluorescent (and sodium vapor, mercury vapor) lighting cycles on and off at a rapid rate. In the U.S., it's 120Hz or 120X per second. In Europe and some other part of the world it's 100Hz or 100X per second.
This cycling of the lights usually isn't visible to us, but the fast shutter speeds of the camera certainly can capture it and camera WB and metering systems simply aren't fast enough to correct for it.
The cycling of the light not only changes brightness, it also changes the color of the light. That's why you are seeing the effect in your images.
Except for your 7DII, which introduces the new "Anti-Flicker" feature that others have mentioned above. Try that and you'll see less trouble with the lighting. The camera will time itself to only fire at the peak of each light cycle.
You did everything else correctly. Your best bet was to shoot in manual mode. And setting a Custom WB was probably a good idea, too. (To se Custom WB, I use a Lastolite EZ Balance target or Warm Cards instead. Two of my Warm Cards are designed specifically for fluorescent lighting.)
Yes, if not already doing so it's also a good idea to shoot RAW (or RAW + JPEG if you have plenty of memory cards) so that you can more easily adjust the color of your images in post-processing. However, you likely won't be able to simply batch correct them all to the same setting. That may correct some, but likely will throw an equal number of the image out of adjustment. That's because the color of the light is actually changing.
You'll find using the Anti-Flicker mode reduces your frame rate a bit... and it will change the timing of the shutter release slightly, might feel like a little bit of "shutter lag" at times. But it's better than the alternative methods of dealing with FL lighting, which are: use flash as your main light source, or reduce your shutter speed to 1/30 or slower to try to capture the full cycle of the lights relatively consistently, or just take a ton of extra shots to increase the odds that some of them will be okay and plan on trashing a bunch.
More info about the 7DII's Anti-Flicker mode here:
http://www.learn.usa.canon.com/resources/articles/2014/eos7dmkii_antiflicker.shtmlAnd here:
http://www.the-digital-picture.com/Photography-Tips/flickering-lights.aspxAFAIK, the 7DII is the first DSLR to have the Anti-Flicker feature. The second link above has some test shots with and without, illustrating how effective Anti-Flicker can be.
I might experiment with Custom WB, the camera's Fluorescent Setting and Auto WB. I'll also be experimenting with the two different FL Warm Card targets I've got, with Custom WB. Compounding the problem, there are different colors of FL light and little consistency (except for the more expensive type that's stabilized especially for photographic use).
Plus, the venues I'm shooting use more sodium vapor lighting, than fluorescent. Though the flicker problem is similar, the WB for that has to be handled differently.