Apenas um palpite. Seu problema pode ser uma grande descarga de página suja. Tente configurar o /etc/sysctl.conf como:
# vm.dirty_background_ratio contains 10, which is a percentage of total system memory, the
# number of pages at which the pdflush background writeback daemon will start writing out
# dirty data. However, for fast RAID based disk system this may cause large flushes of dirty
# memory pages. If you increase this value from 10 to 20 (a large value) will result into
# less frequent flushes:
vm.dirty_background_ratio = 1
# The value 40 is a percentage of total system memory, the number of pages at which a process
# which is generating disk writes will itself start writing out dirty data. This is nothing
# but the ratio at which dirty pages created by application disk writes will be flushed out
# to disk. A value of 40 mean that data will be written into system memory until the file
# system cache has a size of 40% of the server's RAM. So if you've 12GB ram, data will be
# written into system memory until the file system cache has a size of 4.8G. You change the
# dirty ratio as follows:
vm.dirty_ratio = 1
Em seguida, use sysctl -p
para recarregar, descartar os caches novamente ( echo 3 > /proc/sys/vm/drop_caches
).