I know this has happened before and previously with tightserver I solved this by creating an xstartup file in .vnc with -cursor_name left_ptr in it.
Now I have a new stretch image on my new Pi3 with a raspberry touchscreen. Using the VNC that now comes with raspian (configured 'on' in preferences), if I use vnc on my mac with the ip address or the ip address followed with :0 then I get a mirrored screen as per touchscreen with a normal cursor (and the same rather large screen resolution as per touchscreen - despite the setting in the set resolution option). However I can get a different vnc screen, which is what I want, with a different resolution when I issue the following command
$ vncserver :1 -geometry 1920x1080 -depth 24 -dpi 96
and then I vnc from my Mac to x.x.x.x:1 and up comes the VNC screen OK but blast it that blooming big black X cursor is back again. This time creating an xstartup file had no effect. (I did reboot)
Does any know how to get back to a normal cursor in my second VNC screen session.