It make sense to me that compaction should solved this as well since compaction creates new index files.
Am I missing something here?

WARN [CompactionExecutor:1] 2011-04-04 14:50:54,105 CompactionManager.java (line 602) Row scrubbed successfully but index file contains a different key or row size; consider rebuilding the index as described in http://www.mail-archive.com/user@cassandra.apache.org/msg03325.html

Shimi