Yes, I've had a very similar issue. With an SD card in the slot, shut down the computer, when off for > 15 sec, power on, and invariably the CPU utilization will be 25 or 33% depending on power plan in effect. This does not happen with a "restart" of the computer, only with full shutdown and power up. I'm guessing that resuming from hibernation is essentially the same thing.
One "trick" I've noticed is putting the SP2 into sleep mode and then waking from sleep will result in CPU use settling to the normal near 0% level. I'm quite convinced this has nothing to do with the mSD card file system or contents, but rather a firmware bug whereby the mere presence of the mSD card results in an "interrupt storm" and high activity in kernel processes.
I'm in the habit of checking taskmgr after I log in, and if CPU activity is 25% or more, hit the sleep button, and immediately awaken. Taking care with power options and what I'm running on the SP2, battery life is good, averaging ~9 hours per powercfg.