Hi Nathan,
It's Stephen here, we chatted a bit off list before you subscribed.
The first thing to check is that you have setup your application to use SQLCipher. If you are using SQLCipher Community Edition, there is a full tutorial here at
http://sqlcipher.net/ios-tutorial/ on how to setup the application. If you'd prefer to use the Commercial Edition, the setup information is available here
http://sqlcipher.net/sqlcipher-binaries-ios-and-osx.
A good way to check whether your application is linked to sqlcipher is to issue a query for "PRAGMA cipher_version;". If it returns a version string then the linking is correct. If it doesn't, then the app is very likely dynamically linking against the system's libsqlite3.
If you are linking against SQLCipher, are successfully exporting an encrypted database from within the application, have verified that the database is actually encrypted, and are getting a version string back, then there might be some other issue at play. In this case, it would be helpful to see an example of the code you are using, perhaps in a gist, to try and see what is going on.
Cheers,
Stephen