Yes, when there are too many language flags displayed, or the sitename text is too long, then the Gizmo output can fold unexpectedly when long lines are there too. It's a case of trying to fit too much incompressible stuff in the header.
The new V3 template uses a drop-down list for language selection, so is more immune to this kind of overflow issue.
I'd recommend pruning a few languages from your set, then then Gizmo can be reenabled