(damn, I forgot to reply-all again!)
It is also entirely possible that the two things are unrelated, in which case: sorry for any confusion.
But I do know that it is painfully easy to get BOM-heavy files if you use Visual Studio, and that protoc doesn't like it; I can't remember which error message it displays.
I guess the real thing to do is to look at the file as binary: how does it start?