Hey @thomthom …
unfortunately the bug still exists so I tried to fix it on my own. I checked the Ruby Console while pressing on »Clean…« in your menu. This was the output:
Error: #<NameError: uninitialized constant TT::Win32::OutputDebugString>
C:/Users/MARIOSUNSHINE/AppData/Roaming/SketchUp/SketchUp 2016/SketchUp/Plugins/TT_Lib2/debug.rb:36:in `debug'
C:/Users/MARIOSUNSHINE/AppData/Roaming/SketchUp/SketchUp 2016/SketchUp/Plugins/TT_Lib2/window.rb:32:in `block in <class:Window>'
SketchUp:1:in `call'
Error: #<NameError: uninitialized constant TT::Win32::OutputDebugString>
C:/Users/MARIOSUNSHINE/AppData/Roaming/SketchUp/SketchUp 2016/SketchUp/Plugins/TT_Lib2/debug.rb:36:in `debug'
C:/Users/MARIOSUNSHINE/AppData/Roaming/SketchUp/SketchUp 2016/SketchUp/Plugins/TT_Lib2/inputbox.rb:133:in `event_inputbox_ready'
SketchUp:1:in `call'
After that I checked the debug.rb file and commented out line 36:
#Because of the annoying Window Bug in Cleanup³
#TT::Win32::OutputDebugString.call( "#{str}\n\0" )
Now it works again! 
The window is not empty anymore and now I’m able to use it as planned.
But… I’m not really sure if this uncommented Line of Code will affect other ThomThom Plugins?
@thomthom: What do you say? Anny comments?
Greets Mario