Welcome to SOLIDWORKS forums Matthew.
Can you please make sure that plates are not same component i.e. all of three are different parts. If yes and they have an issue, can you please upload them here to check. Also can you make three new plates and try to replicate the issue?
One thing you may want to try is propagate the feature to part. Then open the file with issues, suppress the hole feature and then undo. Finally check. I just remember this workaround done long back.
You might also find this post helpful for your future reference.