To reproduce:

1. Set up a replica set with three members. Initialize it.
2. Add some data so that initial sync happens.
3. Shut down each member and run a repair with mongod --repair
4. Restart the set as usual.

Each set displays this:
Wed Aug 11 13:25:41 [startReplSets] replSet can't get local.system.replset config from self or any seed (EMPTYCONFIG)
Wed Aug 11 13:25:51 [startReplSets] replSet can't get local.system.replset config from self or any seed (EMPTYCONFIG)
Wed Aug 11 13:26:01 [startReplSets] replSet can't get local.system.replset config from self or any seed (EMPTYCONFIG)

In addition, if you look at the original master, collections appear to be missing from the local database:
> show collections
oplog.rs
slaves
system.indexes

This case is also confirmed by the two reports mentioned in this forum post:
http://groups.google.com/group/mongodb-user/browse_thread/thread/56e6f187800a8aef/92a6502ea6be3455#92a6502ea6be3455