Those reports are based on performance alone, not ratings improvements. SInce minor league stats vary quite a bit (because of the quality of players at different levels), I would ignore the stats. Follow tecwrg's advice above. If you see one of your prospects is not getting playing time when the sim manages, keep in mind that the 38 yr old 2b with 50 ratings across the board may be a better player right now than your prospect, and the sim may choose to play the old guy in optimizing a lineup to win, not development. You can play around with the players' primary position to make sure that the guys you want playing are the ones the sim sees as the best first options at that position.
I like to promote at the end of the season, but if one of my minor league teams has a chance at the postseason and the team below it doesn't, I may promote those guys earlier to give them the extra postseason playing time.