I have had the same issue on Windows 7 SP1 (32bit) C::B 12.11; but, I was guessing some other software was interfering with Code::Blocks.
If I get the time might try a simple test case; next time I am at School.
To much junk installed at home to try to narrow done the possible causes.
In my case, CB does not appear to have ever saved the file with the new name.
Note: The only time is is saving for me is when I edited the file.
If I do a File -> "Save File as" of an unchanged file it does not save it for me.
The problem is happening 5 out of 5 trys.
To test, I do a second save as, if the first one works, the second one should complain file already exists.
I just noticed it a day or so ago, I still think it might be a software conflict issue; but, starting to doubt it.
Tim S.