It's part of the job. I was working on a mission scheduled to be launched on Columbia when it blew up. Loss of life aside, that our vehicle blew up wasn't the end of the world. We just used another (which required some adjustment- orbiters weren't all the same).
The cargo bays are laid out a little differently - If I recall correctly, it was mostly due to different styles of airlock between different orbiters. And since the loading on the cargo is highly dependent on where it sits in the bay, you can't just move stuff around willy nilly.
There are probably other minor differences (I want to say there were some electrical interface issues), but that was the part that impacted my work.
Let me guess, your mission went up on Atlantis instead? Being the newest in the fleet I'd expect it to have a different layout from Columbia. Also from your other comments in the thread, sounds like you worked on a Hubble servicing mission, which only Atlantis did after the Columbia accident.
