It could be a plugin that is modifying comment settings. First place to look.
Then look at a new post/page. Are comments enabled for that page by default? (On the page/post edit screen, use ‘screen options’ to ensure that ‘comments’ checkbox is enabled, so you see that setting underneath the post content area.)
Do you get the same results when you change to one of the ‘twenty’ themes?
More info needed, but those are the first places to check, iMHO.
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