The Williamstown cemetery search gives the date of the service for John FLETT as 7 Jan 186
2, not 1861 which would allow for Jane to have been on the
Black Swan in Jan 1861. Unfortunately there are no further records as to birth dates for this person on the indexed Williamstown deceased search so perhaps this is not the right burial.
You probably already know that there are these burials in the Presbyterian section, Williamstown cemetery. I can't get the map to load to see if they are near each other:
James FLETT, burial 25 Oct 1896
Jane FLETT, 10 Jan 1886
John FLETT, 24 Apr 1888
John FLETT, 07 Jan 1862
John FLETT, 08 Mar 1912
There are also two 20th century burials in the C of E section
James Ford FLETT, 14 May 1969
James Ford FLETT, 13 Apr 1934
http://www.gmct.com.au/deceased-search.aspxJudith