The boxes are very likely there but hidden away.
Up to R2014a, uicontrol() always showed up on top, no matter how many things were drawn above them. As of R2014b, the layer is paid attention to, so if you put something above a uicontrol, the uicontrol will be hidden behind it.
Unfortunately, GUIDE is known to have constructed some GUI in which it parented the uicontrol to the wrong layer. For example when a uipanel was created and things were added that were visually on top of that, GUIDE sometimes parented them against the original figure instead of against the uipanel. Then when the uipanel is rendered in R2014b or later, it is visually on top and hides the controls.
You need to go back in to GUIDE and fix the Parent of all of those objects. Or you can write a little bit of code that finds the objects and changes their Parent at run-time. For example if handles.editbox2, handles.checkbox7, handles.pushbutton1, and handles.textbox1 2 and 3 are all intended to be part of handles.uipanel3, then
set([handles.editbox2, handles.checkbox7, handles.pushbutton1, handles.textbox1, handles.textbox2, handles.textbox3], 'Parent', handles.uipanel3)
You would want to do that just after the call to gui_mainfcn() in the first routine in your .m file.
