Since I've always been extremely aware of the way things sound all my life, I instantly noticed the change in timbre of R2's beeping the first time I watched RotJ. It confused me then, and I still don't understand it now. The ones from the first two films sound better.

Part of it does seem to be the somehow more 'childish' tone, and the increased speed. I suspect it also has something to do with the electronic means used to process it. Different equipment may have been used for the third film, and possibly also different choices in EQ.