Hesitating brakes on 2007 Prius

Ever since I bought my 07 prius last August, it has had a slight hesitation when braking from full speed to a complete stop at around 3 mph. I have read that this was due to the regenerative brakes switching over to hydrolic brakes. The slight shutter is supposedly the gap between the regen brakes releasing and the brake pads applying. There is supposedly a software update that the dealership can do to set to where the gap shutter is a smooth transition. It has not got any worse over the last year. I have just learned to brake at a faster rate to where it isn't noticable. I called the dealership and asked for the lead mechanic. When I described what I stated here, he said he has never heard of such events and to bring the car in for analysis. (aka 109 dollars for them to look at it.) I think he does know what it is so they get more business.

There is also an instance where the car drives over a pothole or manhole cover when going on a steep incline or decline and the brakes will actually stop working for a little less than half a second. It has happened to me twice in the last year but I have also read that this is common with Prius cars. It has something to do with how sensitive the ABS system is. Any comments or opinions appreciated!