We are getting "File size mismatch when reading from pack: <filename here>" for multiple files during installation but the files in the Pack are actually not corrupt (and the installation actually works fine if we tweak the resources/packs.info file from the generated jar). The error does not occur with 5.1.2.
Commit https://github.com/izpack/izpack/commit/fc97c51110c771e6b98ca78d21d56c13485bc346 introduced some checks that do not work correctly when a file from another pack within the same jar is referenced during unpacking (com.izforge.izpack.api.data.PackFile#isBackReference is true). That is because the PackFile object and its linked PackFile object have different sizes.
One option is to check the linked file size in the CompressedFileUnpacker (if the file is a back reference). Another option is to copy the linkedPackFile size back to the packFile size in com.izforge.izpack.compiler.packager.impl.Packager#writePacks
Thanks for looking into this. Let me know if I can provide some additional information to help.