I'm running SetupBuilder on a SurfaceBook, which is a 13" screen with a resolution of 3000 x 2000
as such I normally have OS Magnification set higher than 100%

Debug a script
Observe that magnification on Setupbuilder alone, has reverted to 100%
and even that is inconsistent, so now the menu bar is only partially visible (and doubly rendered)

Stopping the debug session does not correct the situation
The only fix is to close and relaunch setu pbuilder

Observed in SetupBuilder version: 10.0.4929 on Windows 10586.71