I am also experiencing this issue syncing over Dropbox:
1Password 6.3.1 (631006), OS X El Capitan 10.11.6 - working
1Password 6.4.4, iOS 9.3.4 - working
1Password 220.127.116.114, Windows 10 Pro - not working (vault is completely empty)
My 1Password.agilekeychain was created on OS X using 1Password 5 (can't remember minor or patch versions). Let me know if there is any other info that could help you. Thanks.
@michaelmatyi: First, make sure you update 1Password for Mac. Then follow the steps in this guide, as it will help narrow down where the problem lies:
I think the primary thing we may need to be looking for is the vault path on each device. If these don't match exactly, then Dropbox will be syncing your data, but your devices won't be using the same data. Please let me know what you find. I look forward to hearing back from you!