I think that if your DR is making a noise, you should open a Trouble Ticket on the iRex website because something is wrong with your device. Mine makes no noise at all unless I press a button in which case it makes a single quiet beep.
I do wish Table of Contents support was a bit better, but the simple fact is that the problem is just as much the fault of publishers as it may be iRex's.
I've used the iRex companion software to transfer my Scribblings to my PC a few times and had pretty good results, especially given that my handwriting isn't that great anyway. I use Adam B.'s Lined Paper Template from this thread: http://www.mobileread.com/forums/showthread.php?t=30872
and have had good results.