@Jammin44fm
OK I've solved it.
The entire application has a Stylesheet applied, including settings for a QMenu, and QMenu item, with custom padding.
By overriding the padding for the specific Menu in question I am setting the left padding to be the check icon size smaller than the normal padding size.
Now when the menu is draw it is consistent in padding size with all other menu's.
I still dont think i should have to do it this way, but it's working.