[NoOne]

possible reasons assuming it's the setup: i'd look at how you have your minor leagues setup. think about using service time limits at the very least in your rookie leagues. if you have alot of minor leaguers with 5-10years experience in your rookie tiers, your freshly drafted players will not likely put up good stats. ltm/lt could mask this a bit, but if this is the problem, autocalculate will not fix this problem because the poorly playing high-potential players are simply not good enough relative to other players in the league. **** i think this inevitably happens during a real-to-fictional transition, in my experience. service time limits help, but you can see a "wave" each year creeping up your minor league (via wins). essentially the Real minors have a lot of middling quality players that fictioanlly created simply never results in. as you switch over, they replacement "filler" isn't as good as it once was... so as those players age and never make the mlb, your minors start improving each year as layers retire (i offer mil extensions but i don't spend time signing mil FA, so i don't re-sign those "types" even though it would improve my mil record the first ~7 years or so

think twice about roster limits -- definitely never use them at AAA... But, who cares if there are 50+ players in one of your rookie leagues, if it does not cause any real problems. this assumes you use "start potential over ability" for your minor leagues -- there's no reason not to. secondly, it's a far better alternative to having a bunch of underdeveloped prospects pushed to the next available level (depends on if you use roster limits above rookie - they could jump to AAA) because there is a 35man roster limit in your rookie league... which do you think has more ramifications? extra on the rookie or AAA team? those players won't develop in AAA and if your scout made a mistake you just lost a quality player (much worse than if it took them a year or 2 to crack a rookie lineup due to bad initial scouting ratings.

becareful of reacting to compulsions to a perception you don't thnk is right... compare the different results and you will see that roster limits are a really bad idea in most normal playing situations. 50 players in rookies doesn't cause any problems with playing time, if you use the potential>ability for lineups in the minors. the other way... there's nothing you can do to avoid the negative ramifications of bumping underdeveloped players above the level they should be in.

all rookie leagues are the same level as far as development is concerned. all A-ball leagues are the same level, except Short A is a distinct level. (just in case this isn;t understood) if they weren't, they'd have their own selection out of the Leage Level drop down list during creation or in edit league settings->League structure area. R -> SA - A - AA - AAA - no other levels... although you can name them whatever you want there are only 5 tiers of competition for standard minor leagues. (you could make a custom game and change default league levels of your various leagues, but that's not the same discussion)

don't look at minor league stats much... especially lower levels and 1-2 months or even 1 season worth of data. not only is the sample size too small to read into anything that they tell you, the players are changing constantly (which taints results), regardless of your choice of time between scouting reports. so, make decisions immediately after a scouting report for best results. pay your scout well, get good coaches*

good coaches - you essentially have to cheat to have any useful information... upto you on that. i'm not sure how "handling" players affects development, but i'd assume the "teach" ratings are more important in the minors. i'd suggest sticking to neutral foci unless you have a very specific player type you almost always draft (even if you think so, i'd suggest still not to do it). Rather, if you have duplicate levels, like 2 A's, then use the second A leauge for coaches with a special focus. send impotant prospects with those specific weaknesses to that team.

Use ratings and not overall/portential. use stats only to verify that your scout is accurate. check out my begginner guide, it has some basic X/100 ratings thresholds for each level of minor leagues... those estimated ratings values are generally bare minimums, but due to scouting inaccuracy you may not be able to follow them exactly.

MOST IMPORTANTLY: if their ratings continue to go up at a good rate, they are fine. use development reports and scouting history in profile. you can see general trends of current and potential ability of the prospect over time - very useful to understanding. in development reports you can quickly see that each scouting update they have a lot of plusses, and few minuses each report and consistently does so.