I recently upgraded to Ubuntu 12.04 from 10.04. My laptop has two hard disks and when I mount the second disk, I no longer have any control over the file permissions (even in su mode). So none of the software I have installed on that disk works anymore. How do I fix this?
Okay, from what I read there you have /dev/sdb4 which is mounted as your root filesystem. You also have /dev/sda2 which is your swap. Otherwise there seem to be no partitions on your hard disk. Which is most likely part of the issue. Please open a terminal, type "sudo blkid" and post the output here. If you don't know how to use a terminal, use google.
Please also use pastebin.com if you want to paste code here. The idea is, that you go there, paste your code, get a link, get back here and paste the link. Keeps everything clean and readable.