Think mail is being deleted from inbox automatically?

I have my aol account routed thru mail. I leave mail in my inbox that I need to deal with later, but I have had these disappear after several days. Like it never existed. Spotlight search doesn't find it either. This has been going on since I started using the mail program in January. It only happens on the inbox; mail I've sent is not affected.
I called apple support about this in February, and was told it reflected a change in the mail of my aol box; that the mail program only reflects what is in my aol box. So I have made sure that I never use aol directly; only go thru Mail to access it. And it is still happening. What do I need to do to keep mail from being deleted? I have had one disappear that I had even flagged.
I checked Mail preferences and the "Keep copies of messages for offline viewing" option is "all messages and their attachments"
What am I doing wrong?
isight G5   Mac OS X (10.4.6)  
isight G5   Mac OS X (10.4.6)   There's usually between 5 and 50 e-mails in my inbox.

I checked via aol webmail. It is not there, either. I suspect it would have been in recently deleted mail if I would have checked within a day of it disappearing, but there were several days where I didn't check my mail, so I missed that window.
I couldn't see where to access mailbox settings via webmail, so I signed on to AOL directly. I checked my preferences for the filing cabinet, and the "automatically delete items in my filing cabinet was not checked, therefore none of the options below that were active. Under mail, save the mail I read, and save the mail I send are checked.
Since I've been using Mac Mail, my filing cabinet on AOL is squirrely. The first thing that happened was all of my saved/incoming mail for over 6 months completely deleted. Since then, it only works "sometimes." It worked most of February, didn't work for several weeks in March (like nothing saved), and worked 3 days in April (4/3-4/6). And I've not changed any settings thru this. This unreliablility is bothersome because I heavily use the saved mail for tracking different items. Any suggestions?
isight G5   Mac OS X (10.4.6)  

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