To be honest with you this is normal. The numbers will never match 100%.
The reason is that traffic can (and certainly does) be lost between two sites even on the same server and also bw 2 different servers on the www.
Same here, I check 2 of my sites trading with each other, the numbers do not match 100%.......
Reason can be various including but not limited to: server load, network load, the network quality (speed) of your network provider, premium network infrastructure vs economy network, php.ini configuration, etc etc.