I guess this was addressed earlier, but would like to bring it to attention again, as it is quite annoying.
By default the record number is used to identify a citation in Word. Unfortunately the record number is not synchronized witht EndnoteWeb. Consequently, when synchronizing via EndnoteWeb on differenty computers the numbers do not match leading to mismatches or at least many changes when formatting the biblography.
The only workaround I found was to create a label and use label instead of the reference number. It would be great if the next version / update of Endnote would have unique identifiers for each entry which are synchronized across all computers.