Passing rustc the --emit=bc flag and passing --emit=bc,link may produce different .bc files (that is, outputs). This is true of rust-core (see below), though was not the case for a simpler ("Hello, world!") test file.

Test script:

#!/bin/bash

mkdir bc
mkdir bclink
git clone git@github.com:thestinger/rust-core

rustc --emit=bc --out-dir=bc rust-core/core/lib.rs
rustc --emit=bc,link --out-dir=bclink rust-core/core/lib.rs

diff bc/core.bc bclink/core.bc

Diff output indicates binary files differ.

Tested with rustc 0.10-pre (0a181a8 2014-03-17 09:57:06 -0700), rust-core on dd0584450. rustc compiled from master on Arch Linux.

If this is, in fact, expected behavior- sorry for the trouble, unexpected to me.