I just installed Code::Blocks with MinGW on my Win7 64 Box and tried to compile a CMake generated project (namely openclonk).
-------------- Clean: all in clonk
Code::Blocks is executing this:
make.exe -s -f <makefile> all
and you are manually executing this:
mingw32-make.exe -f <makefile> clonk
The main difference here is most likely the make target. Re-configure Code::Blocks to make the clonk target instead of the default all. Or, add a target that looks like all: clonk to the top of your makefile (assuming there isn't already an all target defined).
If that doesn't solve your problem, you might also want to investigate whether calling make.exe instead of mingw32-make.exe is making a difference (you can reconfigure this in your project settings).