Here is the continuation of the experiment done previously on Mysql on Windows vs Linux. After doing more analysis and observation, it appeared that the difference in speed for the benchmark tests were not related to Windows and Linux but were related to the processor. The previous test just happened to have AMD 64s on the Linux machines and Intel Xeon 32bits on Windows. We hypothesized that the increased throughput of the 64bit processors resulted in about half the time required to return the same query run on a 32bit machine.
So we decided to test the same query again on a Windows machine with an AMD 64 X2. This time the result for the query took 7.35 second, almost the same as the other AMD 64s running Linux.
One more test to run the query on a Windows Intel 64bit chip machine would better solidify our hypothesis.