I use the "diff" command to compare two compressed files generated using zip on the exact same starting file and they are reported as being different. However, when I uncompress them and use the "diff" command, no differences are shown. I've noticed this with both zip and gzip.
One of the fields in the gzip header is different between the two files. One such field is the last modified time of the compressed file (in seconds since 1970), or if the compressed data was not read from a file, then the time when the file was compressed.
Even a one second difference is enough to make the gzip files not match.
You can use the gzip option
-n) to stop gzip from adding the original file name and the time stamp to the gzip header. That should prevent mismatches when the data is the same, assuming the same compression level is used. One way to add this option to gzip commands is to set the
GZIP environment variable, so that that option is used up by every gzip command. For example, in a Bourne-compatible shell such as bash,
export GZIP="--no-name -6"