The default settings for the "widgets" (buttons?) in the SITE part.
There are settings for the 1x1 widget,
If "you" edit the size of some/any of these, it can cause alignment problems with groups.
Is there an easy (any?) way of adjusting for the misalignment of the adjacent groups?
I would send a picture/screen shot, but my dashboard is "work in progress" just now with some new things, so the problem isn't there.