Trouble quantizing timing of notes from audio recording in Logic Pro X

I am using a Midi keyboard with onboard sounds (Korg Kronos) hooked through USB to my Mac w/ Logic Pro X. I have recorded some audio from my keyboard's sounds as an audio track, and wanted to quantize the timing of some notes.

So I opened the Flex Tool, selected flex pitch, highlighted my entire phrase that I recorded (the phrase has all kinds of types of notes of different lengths) and in the local inspector (bottom of screen) set the "Time Quantize" to 1/1 notes. But when I quantized the timing, I noticed only a slight shifting in some of the notes (transients), but I I would expect the other notes to join such that I only would hear the notes on each quarter-note beat (almost like it's making chords our of my separate notes if that makes sense). But this is not happening for some reason. (i have had no trouble doing this with the midi instruments). Seems relatively simple yet I have tried many different ways and can't seem to get the result I want (which I thought was very simple).

I tried doing this with a drum beat I made up on my Kronos as well, but also didn't seem to fix the timing. Please help!