Clearly, something other than Explorer and Systray is running, without you knowing about it, and it’s hogging all the resources. Luckily, this SHOULD be easy to pin down. While in Task Manager (I assume that’s how you’re checking the resources), flip to the Processes tab and click ONCE on the CPU columnheader. That will sort the list of processes running at the moment by the percentage of processing time they’re using.
Normally, you should see System Idle Process (may vary slightly by OS version) pretty close to the top, if not at the very top. In your case, you’re going to see something else at the top, probably using around 98% of your CPU resources. That’s your culprit. You should be able to End Process on it and see your CPU Usage drop like a rock. But, you’ll still need to locate and uninstall or disable the culprit so that it doesn’t load up again, every time.
My first guess would be an application that’s trying to establish communications with some device that’s no longer attached, but there are lots of possibilities.