In this situation there are likely one or more high-usage processing running In Microsoft Windows which are probably translating into high system usage in OS X. Honestly, every time I have personally seen this happen it has been because an antivirus program is stuck and continually retrying to open a file or resource to exam that it cannot such as a file on a shared drive. AV could also be having a problem with the clipboard in Unity as described in the message below. Another comon culprit is a database program like SQL Server and not having the directory for the database files excluded from the AV program. SQL Server is one example of a program that issues an exclusive lock on a file so the AV gets stuck on it. However, the AV program doing a full scan correctly can also make high CPU usage happen, and the problem will go away once the scan is complete.
To isolate which program in Windows is the problem, open the Task Manager, click on the Process tab and click the button to Show processes from all users, and then on the CPU column to show which processes are using the most. Note here that the Applications tab does not show all the processes running on the system, the Processes tab does. If you have Unity enabled as the view, you can get to the Task Manager from the Control Panel or by clicking on Run and entering taskmgr as the program to run. Normally the System Idle Process should have 90-something percent of the CPU.
Just FYI, and it doesn't show up in the task manager, vmware and Windows do not manage the video adapters on some of the Mac's as well as OS X. For example, on my late-model Mac Air OS X can get as much as 6 hours out of the battery, but if you bring up vmware the run time drops to half. From other posts that I read this seems to be because the video adapter comes up to full power under vmware.
