Hi SW,
Most likely some code/library is in the wrong place.
It would probably help to examine the full command which is being sent to the compiler. In Crossworks output panel there's a way to enable full/verbose output, which shows the full commands used (I forget how offhand... hunt around). This way you can examine the include and lib paths being sent to the compiler, and perhaps spot a problem. Or copy the command which precedes the error and paste it here so we can take a look.
BTW as mentioned in other threads, you may also need to find STM32F4xx_DSP_StdPeriph_Lib_V1.3.0/Libraries/STM32F4xx_StdPeriph_Driver/stm32f4xx_fmc.c in the CW project file list and manually exclude it from the build. Although I don't think that's your current issue.
HTH,
-Max