Columns are added in wrong order
Finally we were able to sort it out: It was a GO in a block comment /* ... GO ... */.

We tested the code in SSMS were the GO is ignored (as it is in a block comment). osql does not ignore it! We had the two batches in this block comment in a previous update. The first was ignored. The second was executed because the GO in the comment broke the comment.

Thanks to @gbn, @JNK and @Brandon for their help!