I have corrected the behavior and the logic now appears to be working as intended.
Prior to the "login type" field a blank user and password would prompt the user for input and this worked fine until we added support for X509 certificates, most servers require a user/pass along with the X509 certificate however awhile back some servers changed this to only require a username and a X509 for access, making the password optional depending on the FTP server and configuration. For servers that didn't require a password it made sense to leave it blank, however as a result FlashFXP prompted for one on connect.
Our solution was the "login type" field.
* Anonymous - no user/pass required.
* Normal - no user or pass required but if the user is left blank then it defaults to anonymous.
* Prompt for password - The user is prompted for the password. if the user is blank then this is prompted as well.
When a site is saved in the site manager the user/pass fields are evaluated and if they were blank the login type was updated to anonymous, but as you can see above the logic indicates that 'prompt for password' also allows a blank user/pass and in this situation the login type should not have been changed.
Please try one of the following depending on the type you're using, I suspect you're using the portable edition..
Download
FlashFXP Portable Edition
Download
FlashFXP Standard Edition
You will of course need to make sure that the login type is set to "prompt for password"