In some cases, a minor difference may be seen in the size of Intermediate/Output files built by IncrediBuild when compared to the same files built by VC.
This is an expected behavior which does not indicate of any significant difference between the files. The reasons for this difference may be:
The OBJ header contains some timestamps/file identifiers.
The OBJ file contains the compiler command-line and path.
OBJ files may include areas of "padding" - big blocks of zeroes that are reserved for incremental updates to the file. This may be different between IncrediBuild and VC builds and explains noticeable differences in file sizes.
Size and content of linked output files may also differ slightly because of padding areas and different linking order of OBJ files.
When running a debug build, IncrediBuild normally uses different PDB files than VC (see KB Article: Why do I see many PDB files in my project's intermediate folder?). This can also lead to differences in the size of Intermediate files.