why do I sometimes see thousands of incoming mail?

I have numerous email accounts (and inboxes)...not sure how that is related to my problem.

I think I have not yet explained my situation very well. I did NOT have 13,332 messages to receive. I retrieve my mail every 5 minutes. I did NOT receive 13,332 emails between retrievals. This is the problem. Sometimes it seems like mail loses track of where it is and then goes "somewhere" to download my entire mailbox all over again. The emails that are being dowloaded are from 2 years ago. Here are a few screen shots:

The first one was from about 10 minutes ago:

This shows the emails sorted in ordder of the Date Received. As you can see, my inbox thinks that there was a gap in messages from 10/10/2011 until today.

Then I had a few of these randomly start in the mail activity box in the lower left corner of the mail app:

BTW, these two screenshots were about 1.5 minutes apart....really at 177KB/S I was still on the same email for 1.5 minutes...I doubt it...but I'll attribute that to the likelihood that the Mail Activity Monitor is really just a "feel good box," i.e. showing me some moving graphics so I think something is happening whether or not the data they are presenting me is accurate.

Followed by this one:

As you can see somehow my mail program found the 3:23 pm, 3:21 pm, 3:18 pm emails from today...when before it didn't show anything between October 10, 2011 and 4:18 pm today. This does not seem normal.

I did sort by the Date Received.

No there are no duplicates.

I have no clue what the Rebuild command is for mail or why I would use it.

I don't know what you mean by "Source of each message," as that is not one of the choices the view menu offers. Since I don't know what you mean by "source," I don't see the purpose of showing this information.

Here is a screen shot of the view by column menu.

And while we are on the topic of me not understanding mail, I also don't understand the sorting mechanism. When I select to sort on name, it collects the "froms" in to a group. But it then it defaults to a secondary sorting mechanism based on the status of the email. In other words, it seems to show the unread ones first, then the ones that have been replied to, then the ones that have been read but not replied to. What kind of idiotic secondary sorting mechanism is that. I would bet that 99% of us want the secondary sort criteria to be the date it was received.

How do I change my preferences so that it does this?

And now that inbox is completely empty....

...and now they just all showed back up in the inbox.

1) I'll so some more research on this. The explaination is pretty thin. It seems like disappearing emails would be a somewhat worrying situation, but Apple's suggestion seems pretty lightweight..."oh well, we lost some of your emails, just rebuild your mailbox."

2) This was a case of word choice. I always show who the email is from...doesn't everyone?

3) We are not yet on the same page. I know how to click the header to establish the primary sort criteria. My question is - How do you set the secondary sort criteria to be somethind useful like the date it was received? The default secondary sort criteria seems to be what action I've taken on the email (not opened, read and replied, read but not replied).

I have simply repeated myself for question #3 because I don't know how to explain it any other way. I do not see how your reply answers my question in any way.