We have isolated the problem
The major difference between Autosys 4.5 and R11 is how the jobs are launched. With 4.5, Autosys is a service that is launched by the internet daemon init (just like telnet, ftp, rsh, etc). The autosys process then execs the batch job requested and off he goes. With Autosys R11, an Autosys daemon is running on the server. When a batch request is sent to the daemon, it does a fork and exec to launch the batch job requested.
On certain servers the xinetd.conf, the umask is not consistent with bashrc (and the other shell files). On these machines, the umask is set to 002 which we believe causes the auto_remote jobs to inherit this setting. However, the R11 auto_remote does not use xinetd.conf. We presume it gets its values in the same manor as anyone else who signs on to the machine i.e. 0022 instead of 002. RedHat 4 machines do not have a umask value in the xinetd.conf. Consequently, we believe r11 and r4.5 will behave the same on these devices.
So, one option we are exploring is modification of the auto.profile to force the umask to match what's in the xinitd.conf file.