Your location with respect to the miningpoolhub server you are connecting to - and the ping time you get could also be a factor here. I live in Australia and I have noticed that if I am mining an algorithm that has a server location in Asia, like equihash for example (and usually a ping time of 50-200ms) - my locally reported hash rate and the rate accepted by miningpoolhub are very similar.... BUT if I'm mining an algorith that only has a hub.miningpoolhub.com port, like Lyra2RE2 - the rate accepted by miningpoolhub is generally lower. I think that this is because you submit many more stale shares when it takes much longer for communication between you and the server. I don't know if this is a fact, it's just my guess from watching the results of mining many different algorthms.
It would be great if there were Asia/USA/Europe connections for everything! Maybe there are and I just haven't read all the info correctly but I think they only exist for the very popular algos like dagger/hashimoto, equihash, scrypt, etc. I think Lyra2RE2 has just taken off recently when Mona and Vertcoin prices went right up.