Unfortunately, this is not unheard of and there's a number of reasons this can happen, such as:
- Your Mailbox(es) are bloated with years and years worth of email data
- an unresponsive macOS at the time (usually due to issues with Mail Data, but also possibly for unrelated reasons)
- a somewhat corrupted inbox
- macOS being unable to find (or having delays in finding) the relevant message data
- unintended consequences due to blocked users or Mail rules
Rebuilding mailboxes was certainly a good place to start. Since that didn't resolve your issue, I would try manually reindexing your mail data.
To do this, follow these steps:
- Quit Mail
- Go to Finder
- Press shiftcommandG
- After the Go to Folder window appears, type (or copy and paste) the following file path:
~/Library/Mail/V9/MailData
NOTE: For users not running macOS Monterey, the "V9" part of the above file path will be different - e.g. for macOS Ventura it will be V10, for macOS Big Sur it will be V8.
- Press return
- The MailData window appears, containing a number of files and folders relating to the Mail app
- Make sure you sort the view by Name (if it isn't already)
- Make a backup of the Envelope Index file and the ExternalUpdates.storedata file (copying them to your Desktop is fine) and then trash them
- You'll probably see other files starting with "Envelope Index" and "ExternalUpdates" - if so, also trash these files
- Open Mail again
- When prompted to re-import your messages, click OK. (Note: You may get a warning that the index is damaged and that Mail has to quit.)
- Be patient while Mail imports your messages. This can take anywhere from a few minutes to a number of hours, depending on how much data you actually have stored locally on your Mac.
Once complete, test Mail to see if this has resolved your issue.
NOTE: If you have any unexpected problems, repeat Steps 1 to 6 above and then copy back the files you backed up at Step 8.