Thank you for the reply.
I got it now, so Ethermine earnings estimate is based on 24 hours data for the rig, while whattomine/miningpoolsprofit are based on the current difficulty.
It makes sense, I will stop thinking much about it.
Its not only that there are other factors as well. For example if you got a slow internet connection then instead of getting a block you might end up with a stale. Another reason is your GPUs might from time to time get hardware errors which are obviosuly never counted as actual shares.
There are also fees with your miner software. Most likely you are paying a 1% fee which you won't see on the pool. Then there is always the chance that your hashrate shown is not extirely accurate either. Depending on what miner you are using might be off by a fraction of a percent or so.
I always take 90-95% of what those values are calculated as my actual earnings.