Indesign shape and pen tool corners staggered

Hi I have an intermitent indesign problem, that is not to do with the stroke or quality settings for the doccument, my shape and pen drawn shapes have an internal stagger to the corners that shows on export to. This happens occasionally but not always. 

Opening a new indesign and copying over doesn't solve the problem?

Is it a hardware issue?

Screenshot showing corners, from a pdf. Looks the same in indesign.