Updating modified link mystery

Just recently we are experiencing the same thing across 3 seats. Everytime we open files we've recently worked on, we get the yellow triangles. Because we've never had this upon opening, it's creating havoc if the user doesn't notice the request to update the link.

We package everything - We file the same way we always have. We store work on Dropbox and sometimes have to sync.

Any ideas on a preference that we need to check or a workaround? Thank you.