2004 Nissan Maxima Auto Trans Problem

I had a new valve body installed in my '04 Maxima. All of the symptoms I was having are eliminated except for a "thud" when downshifting from 2nd to first. The trans shop is saying this is ok, that there is a "learning" period with the new valve body, that this will stop after 100 miles or so. This does not sound right to me. Thuds downshifting from 2nd to 1st are variable; sometimes hardly discernable, sometimes more like a slam and sometimes the car comes to a stop smoothly. Am I getting duped here? Can't afford to lose $2k. Any help would be most appreciated.