just reproduced it, this is what I did :
(tested on linux) :
0) in CB create new console project, build it and close cb
==>
<Extensions>
<envvars />
<code_completion />
<debugger />
</Extensions>
1) open CB, and open the project (I did that by drag and drop from konqueror to CB [no idea if this is a required action for reproduction])
2) Project properties : build targets : I changed for the Debug target the Platforms (unticked : windows)
3) File menu : save project, close cb
==>
<Extensions>
<envvars />
<code_completion />
<debugger />
<envvars />
</Extensions>
4) do the same thing : Project properties etc, an tick Windows back on, then file menu save project, close cb
==>
<Extensions>
<envvars />
<code_completion />
<debugger />
<envvars />
<envvars />
</Extensions>
EDIT : rev 4370