Melodyne 4 Studio produces midi(s) of different time duration/tempo/length from same audio

Sorry no one else has chimed in on your question. I have not done this too much so I am by no means an expert at this but here goes. 
 
If you convert audio to midi using Melodyne and you don't feel that they line up with the original audio then there are a couple of options. you can move the timing of the blobs around in melodyne and then export the midi or once you have midi from Melodyne you could just adjust the midi notes. That seems a much better idea then trying to stretch the audio to match the midi.
 
In my limited experience the midi note on from Melodyne was usually pretty close to the audio but the duration could be off because it has to determine between when the audio event is really off and when it has just decayed to a point where it might as well be turned off.
 
If the Midi data is way off then there might be another issue going on.

Yes. That's actually the preferred way. How were you doing it before?

When you say plug in for the audio track, do you mean like in the FX bin or as a region fx (CTRL+M)?
Maybe you accidentally had different algorithms. I don't know, but at least the easiest way works well!

Here is the durations pic for two audio to midi via Melodyne 4 Studio Demo ver:

each of the two audios, the first midi was from ara, the other three were stand alone melodyne 4 studio demo saved for the melodic, polyphonic sustain, and percussive midi s.