quantizing will fit your loop to mlr’s current tempo, so if you recorded your loop at a different tempo mlr will change the speed of your loop to match (which effects the pitch).
if you activate quantization for your track before recording to the buffer, the loop should be recorded in sync with mlr’s internal clock.
if you want to prepare a loop to load into mlr, just make sure you have made a perfect loop at whatever tempo you wish to work in. quantize your track, load the clip & set mlr’s tempo to match the loop’s tempo.