Sorry, for multiple emails with the same content. There was a delay of over 10h in those emails showing up and I thought they were not getting through.
Regarding the issue. It seems it has to do with the strip phase. I managed to replicate the whole issue outside the build system by taking binaries backed up after install. Then if I run $ strip --strip-unneeded --enable-deterministic-archives file the files can be run fine, but if I use patchelf to add an extra folder to the rpath strip complains like this: $ strip --strip-unneeded --enable-deterministic-archives /home/luk/dev/backup_FileStoreTest strip: /home/luk/dev/stt5WKN1: warning: allocated section `.dynstr' not in segment Then the binary has its elf header mangled as described previously. By copying the unmodified file, modifying rpath and running strip a couple of times I found that there is no problem if the rpath change results in rpath of the same or shorter length, but adding even one byte to it makes 'strip' later complain and mangle the binary. Regards, Lukasz