[ubuntu] Permission on external hard drives

Ubuntu 14.04 LTS

I have two exteal hard drives. Both are NTFS and in all aspects exactly the same, except that one is a 100 GB disk and the other one a 2TB disk. On the smaller disk files are deleted directly, while on the larger one it goes to the rubbish bin. Also on the smaller one I can run scripts that I create or store on that disk even though the owner is root (all text files are by default executable), but on the larger one all text files are by default not executable, and I am unable to change it to executable, even though I am the owner of the file. Why the difference and where can I change these preferences?