Two systems with identical GPUs, have very different performances when running Tensorflow script on GPU

Question

I have two computers with the same GPU(GTX 1080), installed the same copy of OS and softwares. But when I run my tensorflow program(an RNN model), the speed are very different. One is about 1.5x faster than the other.

Here are the key specs of the two:

SystemA: Asus Z170-P, i7 6700T, 32GB Ram, GTX 1080.
SystemB: Asus X99 E-WS, i7 5930K, 128G Ram, GTX 1080. (Problem one)

Both are installed with(using the same method):

OS: Ubuntu 16.04
GPU driver version: 378.13
Cuda version: 8.0
cuDNN version: 5.1
Tensorflow: installed using method pip install tensorflow-gpu==1.0.1
Python: Anaconda 3.6

Sample code:

import tensorflow as tf
import numpy as np
from tqdm import trange

np.random.seed(111)
h,w = 3000, 2000
steps = 1000

x = tf.placeholder(dtype=tf.float32, shape=[h, w], name='x')
t = tf.constant(np.random.random(size=[w, w]), dtype=tf.float32)
m = tf.matmul(x,t)

x0 = np.random.random(size=[h, w])
sess = tf.Session()
for i in trange(steps):
    x0 = sess.run(m, feed_dict={x: x0})

SystemA performs 75 iter/sec and systemB only has 50 iter/sec, yes the poorer one is actually faster.

Key observations:

1. SystemB have a much larger page fault while running the program.
2. By monitoring the Volatile GPU-Util from nvidia-smi, systemA stably seat at about 40% while systemB is about 30%.

Things I have tried on systemB:

1. Upgrade BIOS to the latest version and reset default settings.
2. Call Asus customer service for help.
3. Swap GPU card with system A.
4. Change PCI-e slot to make sure it running at x16 gen3.
5. Inject LD_PRELOAD="/usr/lib/libtcmalloc.so" to .bashrc file.

The main differences of the output of /usr/bin/time -v are:

# The first value is for systemB and the second is for systemA.
System time (seconds): 7.28  2.95
Percent of CPU this job got: 85%  106%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:22.41  0:14.89
Minor (reclaiming a frame) page faults: 684695  97853
Involuntary context switches: 164  91063
File system inputs: 0  24
File system outputs: 8  0

Can anybody point me to a direction of how to profile/debug this issue? Many thanks in advance!

Update:

My rams are Corsair DDR4 3000MHz CMK32GBX4M2B3000C15 which seems like its not listed on the motherboard support list, may be this is the cause? But I have used this computer for a year now, no issues what so ever.

UPDATE:

By a disscussion with stackoverflow user wontonimo, we have found that it is the BUS+CPU casuing the problem. Hopefully someonehere can point to me a direction to fix this. And the post is here.