you need to use ODF (.odt) for that format
Better instructions are here:
http://thedigitalresearcher.com/how-to-use-zotero-with-scrivener-part-2/

that's apparently a well-known issue with Scrivener's ODT export. Two possibilities around that:
1. Export from Scrivener to RTF, open in Libre Office and save as .odt, then run the scan (and the open in LO again to set the reference style).

2. Insert the References in the text in Scrivener. Zotero/Libre Office converts them to footnotes.

I am having two different but related issues.

1. When I use cmd+shift+c to copy a citation from Zotero and then use cmd+v to paste it into Scrivener, the citation that shows up is not correctly formatted. Specifically, the citation I am copying and pasting has an author and two editors, but what shows up in Scrivener is this:

{ | Augustine, et al., 1998 | | |zu:1140854:DKP9E464}

This is how it stays after exporting the document as a .rtf file, converting to .odt in LibreOffice, and putting the document through the RTF scan in Zotero. What shows up in the document after the scan is:

(Augustine, et al., 1998)

However, it should be "(Augustine 1998)." (I am going for Chicago Manual-style author+year format.)

2. After I copied and pasted a citation from Zotero to Scrivener, I manually entered a page number in what I take to be the right spot, i.e.

{ | Augustine, et al., 1998 |147 | |zu:1140854:DKP9E464}

However, the page number doesn't show up any more after I do the RTF scan. Again, what shows up is simply:

(Augustine, et al., 1998)

However, it should be "(Augustine 1998, 147)."

Help! Thanks so much.

You mean in Scrivener or Zotero? How would I do that? Thank you!

In the zotero libre office add-on. This is covered on the instructions, so you can also refer to those.

After scanning the file, you need to open it in libre office and set a citation style (and insert a bibliography if you want one). That's when the actual formatting of citations takes place.

When you say 'scan' is that the same as 'compile'? Thanks