Ok I have had a similar issue, and the solution (if you can all it that) you cannot have 2 Evernote apps say on 2 difference computers connected to the same import folder, ie I have noticed that once it has been imported once, regardless it wont import a second time. This was an issue when using a network share. Only one evernote app must be connected to that folder, and no more. I assume it may calculate a hash for the file so that it does not continue to import the same file from that folder a 2nd time. I now use different import folders for difference computers, and not a shared folder and that seems to have resolved my issues.
Dont know if that throws some light on this subject