Hi. Please make sure that you place the files you want to encrypt in the virtual drive that appears as soon as you unlock your vault in your Cryptomator app.
Do not place your files in the folder that is named after your vault and contains the masterkey file. This is where Cryptomator stores your encrypted files, and this folder is what you sync with your Dropbox account.
Or in other words: Vault is not encrypted - #2 by Michael
Please watch this Cryptomator Tutorial: Get Started - YouTube
And have a look at the documentation.