Jeep Commander begain whining on acceleration. Car shifts rough in first gear. Check engine light in and out. What could we be dealing with here?
Can you get the codes read and report them here?
Most likely you have a bearing going out on either the serpentine belt tensioner, a idler pulley or on one of the components that is driven by the serpentine belt.
But get those codes read and post them here. It may give us more of a clue.
Yosemite
The codes are p0700, p0732,p0733, and we replaced both speed sensors, and the transmission pressure sensor, oil smells burnt. 
Does the tranny fluid look black with a burnt smell?
If so. Not good!
Tester