Compiling previously preprocessed file changes output

I have a source file which I preprocess using the options -E and -P (using GCC 4.1.2 for a vxWorks-based embedded platform). All other options are the same as when I compile the file. These options are: -Wall -march=pentium -nostdinc -O0 -fno-builtin -fno-defer-pop -g -c -o as well as all include-paths. Now when I compile this preprocessed file, the resulting object-file is much smaller (about 30%) than when I compile the original directly. And when I then link the program, the linker complains about missing symbols (all in user-code), which again does not happen when using the original source-file. Why is there a difference? Is there any way to make this work?