Acquiesce,
Whether or not there actually is a problem with Chess isn't the focus of this reply.
Instead, I am addressing your original question concerning the CPU usage. CPU usage for any user apps is indicated in relation to the total of that user's current CPU allocation. In the case of your Chess example, 98% means 98% of
your CPU allocation, not the total of actual CPU capacity.
As needed, and as possible, a given user's allocation will change dynamically, but OS X
tends to keep a healthy reserve held back for additional processes.
To really see what is occurring, perform your test with Chess again, but this time make sure that the CPU "pane" is showing at the bottom of the Activity Viewer window, and pay attention to the percentage of total CPU allocated to you. Chess's usage (98%?) is a percentage of the percentage given to you. As you will see, your allocation will change over time, but it should not approach 100%. So, Chess is using 98% only of what you are currently given.
Now, while this test is running, open another application. What you
should notice is that your CPU allocation will jump, at least temporarily. Also, you should not experience any real "lag" in the response of the new app just because Chess is thinking hard. It is for exactly this reason (among others) that OS X holds that "reserve" CPU potential at almost all times, and this is one of the things that makes OS X such a multi-tasking powerhouse.
Scott