This is not a bug in Toad. I was able to trace the problem and recreate it.

This database was originally set up with full access (select / update/insert/delete) granted to public for all schema objects (Doris). Later this access was revoked and properly set up using roles. Now when we run utlrp, it drops the detail from package bodies. This is verified by querying against the sys.argument$ table for this schema owner. Everything is fine until utlrp is run against the database after the grants have been revoked from public. I've submitted a tar to Oracle. The workaround that we have found is to not run utlrp, but compile each object seperately as needed.