Mac Pro :: Handbrake Encoding Slowdowns - Unresponsive

I ran into a bit of weirdness last night when converting a bunch of Xvid encoded AVI's over to H.264 m4v's using Handbrake. The reason I'm posting here is I think there might be an issue with the hard disk. To begin with, it ran (using 2-pass, turbo first pass) fine, up to finishing the turbo first pass, then it'd hang for about a minute, then carry on with the 2nd pass, running at around 300-400fps (not bad eh!). At around 40-50%, the hard disk starts sounding like it's performing a lot of tasks, even if nothing else is running. fps drops to around 100, then dips down to 30 or so and stays there. Entire system becomes slow / unresponsive. Seeing as the source files and destination for the output were on the same 2Tb drive (25% full), I wondered if perhaps this was too much for one drive to cope with (I'd previously been ripping videos / DVDs to an External drive, and never had this issue). I wiped an external drive, loaded the AVI's, and used it as a source drive, so all my main OS drive had to do was write the file, rather than both read and write at the same time. Same issue, but only for the first file. After this, the whole process ran smoothly. I'm not sure if the issue might have been that I was also copying different files as well as using handbrake, but despite stopping all other activities, this problem persisted, despite reboots, for a while.