Although the Speaker Notes rendering option is active in Vault, it does not appear to be active when documents are uploaded to Vault.
This is working as designed. Some additional notes on how this feature works in Vault are:
If there are no Speaker Notes on the document, nothing appears on the Vault Rendition. This occurs even if they are active on both the Source Document and in the Vault's rendition settings.
Speaker Notes do not appear in Vault the exact way they appear on the source document. On the source document, the Speaker Notes appear in a box below the slide itself. When rendered in Vault, the Speaker Notes are in an added blank space below the slide as shown here:
If there are no Speaker Notes on the slide, the slide appears without the blank area added.
Vault Rendition Documentation: Powerpoint Rendition Options