From my experiences on IRIX, and linux for that matter, just cp doesn't copy all permissions.
It copies the permissions of the file minus the umask. Now does this happen when you
copy just up one directory or does it happen when you copy a file anywhere?
Check your umask, sometimes admins can set the umask in a system environment file..
You might need to set it in your environment files.
After that i would check to make sure nothing was added to your Makefile, that modified
permissions. Not sure if you are working on a project alone, but sometimes people add
stupid stuff in Makefiles.