Check and see what the UMASK value is on both machines:
should generally be the default value (directories have mode 0755, files have mode 0644) -- it may also be 0020 in which case directories would have mode 0750 and files would have 0640.
umask is probably set in
/etc/login.defs; might be worth a look to see what it is.
However, that may not be your problem.
You may want to carefully check (against the manual pages) any settings, changes or additions you made in
/etc/named.con along with the files
localhost.zone,
named.ca,
named.local or
named.root if you're using them (I believe the examples are in
/var/named/caching-example).
Also take a hard look at
/etc/default/named and
/etc/default/rndc if you made any changes to them.
Essentially, files and directories will be created by utilities with whatever mode is defined by UMASK on the system; if you have added or changed anything having to do with file and directory creation, that's probably where you need to look first. Carefully check your configuration files (the ones having to do with master-slave).
Hope this helps some.