Whining noise and shifting issue

I have a 1999 Infiniti QX4 with 250,700 miles. I had the transmission replaced about 2 months ago. It is the second time. Recently, it has been making a whine noise when accelerating. I heard it once a few weeks ago and figured I had just never paid attention before. Then it got worse when I noticed it again a few weeks later. The pitch of the whine follows the RPM range. Also when I got the car back, when shifting, you could definately feel it shift from gear to gear. This morning when I drove it, as stupidly as this sounds, now it is shifting too smooth. When the rpms shift back, it seems slow and you hardly feel it shift now. When it is shifting full throttle, it hesitates a little as well, but slowly shift to the higher gear. What could be causing these?