I'm using an intervalometre. Looks like it was mirror slap. Strangly live view helped, I say strange because on the D3300 in live view when a picture is taken the mirror is released back down and then the picture is taken as normal with the mirror coming back up to expose the sensor. Technically it should have made it worse as there is an extra mirror movement. Anyway I've eliminated the issue.
Thanks everyone for the help.
PS: In live view the battery was being consumed very fast, I've found the settings to turn off the preview screen and have recorded several hours of photo's @ 1 frame every 3 seconds.
http://www.henrywho.xyz if you want to check out some of my work. The Fuji is a little $69 14 Megapixel pocket camera with 3x optical zoom that I take in the top pocket of my work shirt when on the bike or in the 4wd, most of the pictures are quite hurried.