Какой жесткий диск (диски) находятся в сервере? можно быть более обеспеченным удалением их и попыткой получить доступ к данным путем помещения их в другую систему как вторичные диски.
Can you post jMeter profile - depending on your cookie configuration, you will find differing results from EE's FPC
Also, how have you configured your cache backend, to use File/Backend/DB/Memcache/Redis? http://www.sonassi.com/knowledge-base/magento-kb/what-is-memcache-actually-caching-in-magento/)
Both of the above points will effect the frequency and type of SQL queries being executed. But I wouldn't rely solely on FPC - especially when benchmarking. It makes a lot more sense to disable FPC but leave the remaining caches enabled, so as not to skew your benchmarking.