Windows7x64, 4 cores, GPU.
BOINC 7.0.64

The last few days or couple of weeks it seems project exes don't obey the computing limits I set up (90% of total CPU time), and were hogging the entire computer. Projects that seemed to especially offend were Chinese Academy of Sciences and EDGES, but I'm not sure it was only those. I've removed those two and continue watching.

I've used BOINC for a year or two now and this is the first time I've seen projects not honoring the limits.

You might want to indicate the projects you are actually running, especially any GPU projects.

If you have 4 cores and you tell Boinc to only use 75% of them, it will use 3 cores. If you say 90% or even 99% it still means use 3 cores. The GPU usage tends to be an estimate, and not always accurate. Some GPU WU's use high amounts of the CPU during some stages of the run, especially at the start, and lower amounts at other times. Overall it might be fairly low, but at some stages it will be a full core. Do you observe this behavior when a GPU task starts?