Thanks guys,
I changed the video plugin to rice and it now works from the command line, but when i launch it from emulation station it comes up with the error

failed to append config “/opt/retropie/configs/n64/retroarch.cfg”

and loads up in default mode which is n64 with the crashed screens. From what i can tell this is an issue with multiple configs in retroarch as buzz stated in another post here

does anyone have n64 working currenlty with the 2.6 image?