Ubuntu :: Won't Boot - Possible Data Corruption?

I'm having an interesting issue with my computer right now. It has Ubuntu lucid installed, which was upgraded from karmic shortly after it became available and was up to date as of September 1.

The issue is as follows: It will not boot the internal hard drive (250GB Seagate barracuda). When I select any of the kernels, it appears to be booting, but 6 Hours later, no joy. If I select any of the Kernels in recovery mode, it does nothing, so again no joy.

It will boot my 500GB removable drive via USB (Samsung on the inside), which contains a backup of my lucid (cloned with Clonezilla) from June-ish, but will not do so if the internal hard drive is hooked up, so I cannot access the internals contents while using the backup USB HD.

Now this is where it get's interesting, at least for me. It will boot up a livecd while the internal HD is connected, which was the only way for me to access the contents of my Ubuntu partitions in the internal HD. I have since pulled the Internal out, removed the USB 500GB HD from it's case, installed it into the internal HD bay, hooked up all the cables, turned the computer on and it did boot. While it did seem to take a long while to boot, I'm hoping this may be because it needs a serious amount of updates (294 updates, 485MB are ready via synaptic!). So I now have placed the 250GB Seagate into the USB HD case and can now access it, but the only contents that can be seen, are the items in my defunct vista partition and I cannot find any remnants of my Ubuntu installation, despite gparted being able to see all of the partitions.