It's possible that something in the xml file is corrupt. Having all of the non-pitched percussion notes to the same midi number is a clue. It may also have to do with how the sib file is saved/exported to xml.
When you say you're both using the same Write Score templates, what do you mean exactly? There are templates for Finale and Sibelius. Each has different systems for percussion layout, mapping, and playback with regards to VDL.