I still think it's normal, one core is hogged with mining, the other is doing system related tasks.
The system related task take 3-4% always when i'm not mining and so+i don't play any games that would use resources and so.
To be clear, does bitcoin-miner show 90% processor usage, or is 90% processor usage shown in total with bitcoin-miner showing 50% cpu usage? There are no system related tasks using processor as bitcoin-miner, and in my experience, it has practically no overhead, so if it shows 90% something is wrong in this particular instance that is not other system related tasks but specifically related to the miner, either not using one thread or having far more overhead than typical.