So I'm having this weird issue on the dashboard where custom permalinks only (default, day and name, month and name etc. those all work fine) doesn't save. I can choose the radio button and click "Save Changes" and the radio button will revert to one of the previous choices that works fine.
And so I found this online which suggests to add index.php preceding the link, and it works now - but I feel this fix is a "bandaid" of sorts and doesn't actually resolve the issue. Are there any repercussions of using index.php in the custom permalink structure?
Also, if it helps, the site was updated from 3.4.1 to 3.9.1, no PHP errors, all plugins are disabled, and there was an htaccess file missing, but I put one in using this. I am also seeing the htaccess actively update whenever I choose one of the options that work so it's writable.
Any idea why only the custom permalink structure is an issue and can I safely insert index.php into it as a fix?