I also found that the devs actually do not recommend running the x64 version of arma server. There are instances where it works fine, but it is a chore to maintain. (probably why it is not in the documentation)
If you switch over to extdb2 and armaserverx86 it should work fine though if you have all else setup correctly.
You may have another issue. I would recommend uploading your RPT log to Pastebin or something for review.