Was there any sample rate conversion involved? Did they provide documentation confirming what sample rate all the files were at?
If it's none of the above, the only thing I could imagine is that someone screwed up doing the consolidations in Nuendo. The thing with Nuendo is that there are several potential ways to consolidate and/or export files, and they don't all work the same, so if the recording engineer is a recent Nuendo convert he/she may not have consolidated/exported properly.
What the wise man does in the beginning, fools do in the end.
The four most expensive words in the English language are: "This time it's different."
--John Marks Templeton