It seems that when I start a mongod with --auth, then do db.setProfilingLevel(2) and a find(), nothing is stored in system.profile. Repeating the same test without --auth succeeds.

I run the attached test_profile.sh against a mongod started with and without auth:

$ mongod --dbpath ./data/db4000 --port 4000 --logpath ./log/db4000.log --fork
$ bash test-profile.sh
MongoDB shell version: 2.0.1
connecting to: 127.0.0.1:4000/test
dropping system.profile
true
profiling level=
0
setting level to 2

{ "was" : 0, "slowms" : 100, "ok" : 1 }

find

{ "_id" : ObjectId("4f1ee0ca17b5b6b96b6ec15d") }

setting profiling level to 0

{ "was" : 2, "slowms" : 100, "ok" : 1 }

db.system.profile.find()
{ "ts" : ISODate("2012-01-24T16:48:10.395Z"), "op" : "query", "ns" :
"test.test", "query" : { }, "nscanned" : 1, "nreturned" : 1,
"responseLength" : 42, "millis" : 0, "client" : "127.0.0.1", "user" :
"" }
{ "ts" : ISODate("2012-01-24T16:48:10.395Z"), "op" : "command", "ns" :
"test.$cmd", "command" :

{ "profile" : 0 }

, "ntoreturn" : 1,
"responseLength" : 58, "millis" : 0, "client" : "127.0.0.1", "user" :
"" }
bye

$ mongod --dbpath ./data/db4000 --port 4000 --logpath ./log/db4000.log
--fork --auth
$ bash test-profile.sh MongoDB shell version: 2.0.1
connecting to: 127.0.0.1:4000/test
dropping system.profile
true
profiling level=
0
setting level to 2

{ "was" : 0, "slowms" : 100, "ok" : 1 }

find

{ "_id" : ObjectId("4f1ee0bd5f245c46ab557b47") }

setting profiling level to 0

{ "was" : 2, "slowms" : 100, "ok" : 1 }

db.system.profile.find()
bye