If you change 'Object file extension', either by directly modifying the corresponding field in 'Compiler options' or switching the currently used compiler to one with such already-changed settings, Code::Blocks will still tell the compiler to generate the old file extensions for new object files everytime, until you restart the IDE.
I haven't tried to find out if other options also affected with similar problems, honestly.
Related to [#128]
Related
Tickets: #128