I have been shooting indoor high school basketball for a couple of years now. I am curious when (what time of day) you took your practice shots. I ask because, in my experience, in Jacksonville, Florida, the games are taking place after 6:00 in the evening, in the winter time. This means that, while you can get situations where you have sun coming in some windows in the gym, creating odd lighting conditions for short period of time near sunset, the bigger issue for me has been an overall lack of light. Some of these high school gyms are seriously dark.
I do find that using spot metering, tends to give me optimal results in those moments where there is residual daylight to worry about, so I recommend trying that and using either aperture priority or shutter priority.
You will not have this problem because you're shooting with a 1D Mark IV, but because I shoot with a 40D (soon stepping up to the 1DX), I have had to shoot with shutter priority in order to stop the action. Aperture priority would result in too slow a shutter speed most of the time (for my camera). I cannot shoot at ISOs higher than 6400 at all, and at 6400, I get some pretty bad noise. So, with this old camera, I tend to get shots which stop the action but are under-exposed initially. Then I can boost the exposure and deal with the noise in post. As you might imagine, I am REALLY looking forward the the major improvements that will come with the 1DX.