Breadboard Layout Doesn't Line Up

I don’t know if this is a bug or just a problem with my being new to the product. Many times, in breadboard view, when I add a component to the board, the pins of the component will not line up with the pins on the breadboard. Often times they are spaces a few pixels to the right of the hole they are “in”. Occasionally, with resistors, the “active” hole is actually before the pin. I can usually fix the issue on LEDs just by rotating them a little, but on other components that doesn’t work. Has anyone else had this issue, and, if so, how do you fix it? I am running 0.9.3 on OSX El Capitan.

NOTE - sometimes it works fine, and I can’t figure out what I do that causes them to shift.

Have you got View/Align to Grid ticked.