Is there a reason Synchronize wouldn't be working correctly? I've had a few instances recently of Synchronize frames ignoring the Synchronizer. Yes, before anyone asks, I'm 10000000% sure the Synchronizer was the first Pokemon in my party, and it did have the correct ability.
Example: Using seed 8E667B89AD18D0EE, aiming for frame 249. I was able to get the
shiny Metagross I was looking for, but it wasn't Adamant. Also, my shifted starting frame was 57, which was also a Synch frame, but I got Brave instead. This was in Black.
Another example: Seed C6C59DF072AEBA14, frame 127. I got the shiny Trapinch, but its nature was Modest instead of Adamant. This was in White 2.