How far back are you comparing with?
It seems fleet training rules were changed for 6.40 in around mid 2014 according to the change log:
Fleet Training Change
Fleet Training rate is currently based on task force commander's crew training plus half the operations officers crew training. For v6.40 this is changing to task force commander's crew training * task force operations bonus. The latter is equal to the operations officer's operations bonus * 25% of task force commander's operation bonus.
So if the TF commander has crew training 200 and ops bonus 10% and the operations officer has ops bonus 20%, the fleet training rating for the task force will be 200 x 1.05 x 1.20 = 252
This might explain what is happening here since:
Using 6.30 rules you would be getting 125+375/2 = 312.5
Using 6.40 and later you would be getting 125 x 1.? x 1.? = much lower ( likely around half ).
You probably still should see some good progress where you have task force commanders with 250 crew training, so I am not sure what the issue might be with those.