Just registered here to say I'm experiencing the same issue as well.
I've been mining for 2 day continuously, claymore's miner reports almost constant hashrate of ~700 MH/s yet on nanopool it shows ~600 on 6-hour and even 24-hour averages.
So, I stopped mining completely for 1 hour then restarted for 1 hour then stopped again and counted the number of (accepted) shares.
On nanopool the sum was around 18% lower than what shows up on the miner.
WTF is going on ?
(BTW, I'm also getting around 1% rejected shares, but that's clearly not the issue here)
Umm...looks like you're experiencing the same issue.
The reject rate is high but won't cause so much difference.
Accounting to your measurement on share difference, I guess there are two possible situation.
1. Nanopool take some shares as 2% commission fee.
2. The worst case is if the difference is much more than 2%, then it might be some "disappearing" share(hashpower lose) between Miner & Nanopool's communication.
Anybody else has the same issue? Or got any idea about it?