What's the meaning of 'TRWTF '?

It means:

The real "What the F***"

Which is:

What is really bad about this, where they really blew it was...

WTF is an abbreviation in its own right and could also mean

What in the world, what in God's name

Therefore TRWTF would express

The reason one might exclaim "What in the world is this", is that they were running as root, at a nuclear sciences research facility.

For the origin, see Claudiu's answer.

Ralph's answer has got the meaning. As to the origin... there is a website, www.thedailywtf.com, which has daily posts of really idiotic and messed up coding practices. Usually the story is obviously terrible in a certain way. However, people say "Well, the real wtf is..." meaning, the thing that is really messed up.. and they point out something more subtle/funny.