For what it's worth, I had syncing problems too.
I think I solved this by not using my username anymore but use my emailadress to log in.
History:
I had installend Evernote on multiple PC's, my iPad and iPhone.
On my PC's I installed the new version 10 and, because of slow performance of version 10, also side-by-side the legacy edition.
I found out on the same PC the version 10 and legacy did not sync. Even worse, there appeared a few hundred notes in my inbox on my PC's which I had moved earlier.
In the end I removed version 10 because of the sync problem, this did not resolve the sync problem between my PC and the web-version of Evernote.
I then decided to disconnect (log out) all my PC's, iPhone, web and log back in with my email-adress and not use my username, this solved the sync problem !!!!
I used on some of the PC's my emailadress and on some my username, I did not think this could be a problem but maybe it is.
Just to be sure I removed Evernote from my iPad and iPhone and reinstalled Evernote again.
While syncing I saw my inbox being cleaned from 493 notes back to the 2 there ought to be.
Hope this is of use for some of you.
Greetings Eric