I had the same problem. The following blog post helped me resolve it:?http://www.polak.ro/svn-e200030-sqlite-database-disk-image-is-malformed.html
You do an integrity check on the sqlite database that keeps track of the repository (/.svn/wc.db):
sqlite3 .svn/wc.db "pragma integrity_check"
That should report some errors.
Then you might be able to clean them up by doing:
sqlite3 .svn/wc.db "reindex nodes"
sqlite3 .svn/wc.db "reindex pristine"