I recently cloned my old HDD to a new smaller SSD and something must have gone wrong. Windows 7 works absolutely fine, but Ubuntu 12.04 has issues - at first, it works normally, but after only a minute or less the filesystem locks up. I can't open any applications other than the dash and file managers, if I try a sudo command in console I get a read-only error on /var/lib/sudo/alex. Other problems like this generally seem to be related to an old or degrading hard drive, but that can't be the case as my SSD is brand new. I launched recovery mode and used fsck, it found a few errors but it didn't fix the problem.
Here's the steps I used to clone my HDD to the SSD (did it partition by partition):
1) Cloned Windows Recovery (sda1) and Windows (sda2, boot) to the SSD with Clonezilla.
2) Copied the Linux (sda3) and LENOVO-PART (sda4, diag) partition to the SSD with GParted Live.
3) Got the Windows Boot Manager error on startup, used a recovery disk to restore Windows' boot manager (Windows works fine now).
4) Used an Ubuntu Live USB and the boot-repair utility to install grub2 to: sda and sda3 (it didn't offer sda2, which is the boot drive, but grub seems to work fine).
It may be that copying the partitions using GParted misses some crucial information or is messy but I have no idea why that would be. That being said, Windows works fine and I used Clonezilla for it, whereas I used GParted for Linux. This is for a laptop so setting it up to clone requires taking apart my desktop and pulling a bunch of plugs so I'd only like to do that if I knew it would work right.
Any thoughts on the matter?