Try removing mlocate, this may impose _great_ load on your IO.
Also, please install "sysstat" package and enable it in /etc/default/sysstat.
When some time passes, run "sar" - it will show you when the server is loaded and when it's not.
Typically, it can be some cronjob.
you could just configure mlocate to ignore different (and large) directories as well -
our sar showing:
time: device read/s rdKb/s write/s wrKb/s rdwr/s _disk_
04:30:01 disk008-000 89.94 2588.18 166.91 4240.67 256.85
04:40:01 disk008-000 68.29 1275.69 155.94 4317.52 224.23
04:50:01 disk008-000 9.31 121.69 160.23 4338.11 169.54
05:00:01 disk008-000 8.72 124.08 161.72 4120.00 170.44
05:10:01 disk008-000 8.28 171.14 160.45 4054.25 168.74
05:20:01 disk008-000 12.34 303.10 188.17 5054.48 200.51
05:30:01 disk008-000 7.18 102.60 159.01 3643.48 166.19
05:40:01 disk008-000 11.57 103.96 170.11 4103.74 181.68
05:50:01 disk008-000 8.25 131.66 165.02 4162.74 173.28
06:00:01 disk008-000 127.42 11700.96 161.66 4602.04 289.09
06:10:01 disk008-000 245.13 1398.37 159.30 4771.15 404.42
time: partition busy read/s Kbyt/r write/s Kbyt/w avque avserv _part_
04:30:01 sda (8-0) 64% 89.94 28.8 166.91 25.4 17.08 2.50 ms
sda2 611.45 4.2 1060.15 4.0
04:40:01 sda (8-0) 45% 68.29 18.7 155.94 27.7 13.37 2.00 ms
sda2 293.59 4.3 1079.36 4.0
04:50:01 sda (8-0) 18% 9.31 13.1 160.23 27.1 6.96 1.03 ms
sda2 10.67 11.4 1084.52 4.0
05:00:01 sda (8-0) 17% 8.72 14.2 161.72 25.5 5.46 0.97 ms
sda2 10.62 11.7 1030.00 4.0
05:10:01 sda (8-0) 17% 8.28 20.7 160.45 25.3 7.73 1.02 ms
sda2 9.81 17.4 1013.56 4.0
05:20:01 sda (8-0) 23% 12.34 24.6 188.17 26.9 9.10 1.13 ms
sda2 15.93 19.0 1263.61 4.0
05:30:01 sda (8-0) 15% 7.18 14.3 159.01 22.9 5.85 0.93 ms
sda2 8.34 12.3 910.87 4.0
05:40:01 sda (8-0) 22% 11.57 9.0 170.11 24.1 7.69 1.19 ms
sda2 12.57 8.3 1025.93 4.0
05:50:01 sda (8-0) 18% 8.25 16.0 165.02 25.2 7.01 1.04 ms
sda2 9.57 13.8 1040.68 4.0
06:00:01 sda (8-0) 58% 127.42 91.8 161.66 28.5 12.94 2.01 ms
sda2 172.65 67.8 1150.51 4.0
06:10:01 sda (8-0) 99% 245.13 5.7 159.30 30.0 8.52 2.45 ms
sda2 252.43 5.5 1192.80 4.0