It’s really hard to know exactly from your description. The way it’s supposed to work is.
1) Install AxCrypt.
2) Sign up with your email, verify your email with the 6-digit code, set your password.
3) Sign in with your password.
4) Encrypt your files.
5) Exit AxCrypt for whatever reason.
6) Start AxCrypt, sign in with the same password you used before.
7) Encrypt or decrypt your files without specifying any more passwords.
Not sure where you diverged from the above in your case. Can you perhaps send a screen shot of the situation?