Yeah, it all seems to stem from the player pages.
Have a look here - the EL is the actual MLB level for this save, but it is allocating his COL and AAA stats to the MLB TOTAL in the summary, and that is what is apparently appearing on the sortables. Just the WAR is wrong still, the other stats look OK to me except it also doesn't seem to be allocating career highs for the averages - although that might be because he hasn't had enough qualifying PAs yet?
Please note, Matt, that when you just select the actual League under SCOPE in the sortables, rather than "Major League", the correct figure appears. To the OP, this might give you what you need in the interim until it is sorted out properly.
