This same DeDRM'd file can be viewed by Calibre but not converted by it, which suggests that you are right.
So there must be a problem DURING the conversion process, which goes back to what I said earlier that it is a programming-related issue.
Damage must occur when Calibre extracts the data (from a DeDRM'd file) and tries to re-compile it.
I'll test this theory on a large, non DeDRM'd file and let you know

Or, the original file may be corrupt/damaged, which as a programmer, I know a lot about. You may be right about there being a problem with the original file. Not that I produce corrupt files, more that I have had a fair amount of experience with them