This happened to me every time I made 10-15GAL batches where I would prematurely keg 1 of the 2-3 fermenters due to lack of beer.
The first keg would be delicious. I'd then let the other fermenters sit for the full duration, cold crash, and keg. Those kegs would have a considerably different flavor profile...enough to think it was a different batch of beer.
I've also noticed this doesn't happen with heavier, more complex beers, only light ones.
So, I've come to the conclusion that light body beers should be fermented and kegged in as short a time as possible...so they are green and fresh...no aging at all. Cold crash in the kegs and pull the first glass off to get as much sediment out as possible.
That last comment is strictly my opinion based on my personal taste in beer. Some might disagree as they prefer a different taste profile.
Now with a single 20GAL fermenter, I have to process all the beer at once so I won't see the drastic change in taste between fermenters.