On a fresh installation of siteminder (unix) running v12.52 sp1 cr04, running smconsole sporadically corrupts sm.registry by changing the policy store location from LDAP to ODBC. The next time the policy server is restarted, it fails. This has happened, but not limited to the following situations:
1. Changing LDAP policystore hostname
2. Changing tracing configuration
Suggest you keep backups of your registry, as there may be other items which get altered.
I've seen it too. Went into smconsole to change the profiler settings, and restarted the policy server a few minutes later and it wouldn't come up, because it was failing to connect to a data source. It had switched the policy store from LDAP to ODBC. Strange behavior