I use 2-3 different setups all with mlat, never had an issue
depending on the antenna different ‘syncs’ are shown, with
most related to the better / more sensitive antenna.
I run 2 receivers from time to time. The only glitch I noticed is that when you disable MLAT on one of them, the FA page still shows MLAT active for that receiver.
My guess is that since they both have the exact same coordinates, it confuses the MLAT ‘robot’.
Are you using the same feeder-id for both? I think I tried that once, just to see, and it did not work.