@aguynamedben - the new release of SQLCipher 4.2.0 adds PRAGMA cipher_integrity_check. It performs an independent check of each page in a database using the stored HMAC, and produces a list of an errors found. It might be a good idea to collect some information when these errors occur. If no problems are found with the “envelope” of the database by cipher_integrity_check, yet the database it is being reported as SQLITE_CORRUPT during use, then it is likely that some problem corrupted the database internally (e.g. logic error, improper use of the database API, etc.).
Let us know when have a chance to put together that sample application.