1. have mongodb 2.0.3 installed.
2. run the daemon with sudo rc.d start mongodb
3. upgrade mongodb to 2.0.4
4. try to stop the daemon with sudo rc.d stop mongodb

It prints FAIL and in /var/log/mongodb/mongod.log I get:
"Process 3604 is running /usr/bin/mongod (deleted) not mongod"

The problem here is the line at:
https://github.com/mongodb/mongo/blob/master/src/mongo/db/db.cpp#L1043
"else if (!endsWith(buf, "mongod")){"
My buf ends with "mongod (deleted)"

Note, the daemon is using the mongod --shutdown flag to stop the daemon.