SQL Compare 12.4.9.4945 - Ignore comments not working

I updated SQL compare today to 12.4.9.4945. When I ran the compare this morning, I had 5 or 6 changes to examine. After the update, I have 177. They new changes are comments, or possibly whitespace/commments changes.

I have the settings for ignore comments and ignore whitespace turned on. Is anyone else having this issue?
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