Sometimes applications try to access protected folders without prompting from the user, resulting in the password prompt appearing when you don't expect it to.
For this reason Espionage has an ignore list which you can access from the Tools menu in Espionage.
Important: whitelisted applications do not necessarily have access to the folder's contents! Encrypted folders have their contents stored inside of an encrypted disk image, so that is what a whitelisted application would see, and not what's inside the disk image (the actual contents of the folder). On the other hand, if the folder is not encrypted, then they would have access to its contents.
To add an application to the ignore list simply drag it onto the table or click the add button to find it. You can also add an application to the ignore list from the password prompt.
Below we've whitelisted the backup program SuperDuper! so that it can backup our encrypted folders without triggering the password prompt:
You should add any regularly scheduled backup applications to the ignore list to prevent delaying their execution. For more information on this see "Backup Software".