The chkstat program is built without large file support (-D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64) which can make it silently fail if it runs in a 32bit
userspace on filesystem of a 64bit host.
The code just silently fails:
https://github.com/openSUSE/permissions/blob/ece8520ae271152d88ad24968c3831417ce4732c/src/chkstat.cpp#L950

I ran into the issue when building i586 packages on x86_64 when /var/tmp ended
up with values that stat couldn't digest so was silently skipped and left with
wrong mode. As you can imagine that leads to mind boggling build fails :-)
Please compile with LFS.