You might want to try the following:
* Check the add-on version # you're using
* Equip all spec's in-game before exporting data - incl. 'opening' all Artifact weapons you have
* Check spec. priority in AMR to match what you're playing, incl. any custom gearing parameters (Instance levels, iL scope, etc)
Synch your character with the Armory so that the data string you import from the game doesn't conflict with what AMR has cached your character as having geared with - the data-string you import doesn't override the cached data on your last Armory import.
Finally, factor in that AMR, like other sources only 'advises' you what is BiS; no site that offers this kind of help is perfect, as no two players with the exact same gear will play 100% the same, 100% of the time... humans are not that perfect.