Without knowing what vehicle you have it is hard to give an educated answer, but generally if there is a problem with the clutch then it will show up every time you shift, not just in one particular gear. Since it is a hydraulic clutch there should be no real adjustment to do. It would also be useful to know why the old clutch failed. If the input shaft seal leaked and ruined the clutch disk, it is possible the fluid ran low and there is some damage internally to the transmission. Again depending on what vehcile you have, if they had to pull the transmission out to get at theclutch it is possible they damaged the shifter or some debris fell down inside and got into the second gear shift rail.