I have two external hard drives. One is a 2.5" 80GB USB HDD and the other is a Seagate 3.5" USB 500GB HDD. Both hard drives are mounted properly and I can access the data on both hard drives. I can access the small 80GB HDD via ssh from another computer and delete files, but when I try to access the 500GB drive via ssh it says access denied. When I try to access it with root, I can access it but I cannot see any files listed.
Further to what syampillai noted, you could provide more information by typing (with both external HDD connected) and providing the output from:
df -Th
cat /etc/fstab
su -c 'fdisk -l'
you will need to enter the root password after the last.
Note also if the external hard drives are NTFS formated, and if they have errors on them (requiring an MS-Windows chkdsk), and if they were not removed/umounted properly in MS-Windows, then there is a good chance Linux will not see the contents.