It might be your cache settings combined with the RAM upgrade causing much of the above. Maybe there's nothing wrong with the hard disks:

- Icon indicating data is being constantly read.
- Occasional glitches as it spends too much CPU time trying to fill the cache.

Everyone else: Is there a way to tell the software to behave exactly as if he didn't have any RAM upgrade at all?

If so, try that, and see if all your problems go away.