(just in case) The PQ Editor only provides a preview of the 1st (1K top of my head) rows. Not sure what else to say given the information you provided (no query code)
Merging and Grouping operations cannot guarantee an order set of records. If you do any of them this could explain what experience
Other thing, do you Add to the Data Model in addition to loading the query output to a worksheet? It took me a moment to find it out but this case I dealt with some time ago reminded me something...