I have updated my U++ IDE to version 6254 and it seems that this issue is back. Now, even when I specify compiler flags, some of them get overwritten by the default TheIDE options. For instance, if I set /Ox (maximum optimisation) for Visual Studio 11 x64, I get
cl : Command line warning D9025 : overriding '/Ox' with '/O1'
I have switched back to an older version and it works fine. It seems to me that the new Visual Studio 11 support adds this, to me undesirable, behaviour.