Heck, I couldn't even find any tagable crates! So much for a quick Commander ding.
UPDATE: SNAP! I shoud have logged instead of beaming out! Now I have to do the whole friggin' space combat over again!! GRRRR!!! And, just as I thought happened the first time, S'laraen isn't in the room where he's supposed to be; last time I swear he appeared later, magically, after some unknown criterion was met.
I found this thread because I thought it was bugged for me too. I couldn't find any crates. Turns out they were all in the last room, hidden in the big stacks of boxes. You have to really look for em, they don't look like the rest of the crates in the station. So if you think your mission is bugged, just give that room a REAL thorough search.