dont know if this helps but it sounds like you are having the gmail problem ... any time a client downloads a whole message gmail marks it as downloaded and archives it ... then the next time you check your mail the client doesnt see anything ... probably a scheme to keep bandwidth low and you cant blame them
... when you use the recent command that ECNiz talked about (recent:<username>@gmail.com) it forces gmail to download all e-mails from the last 30 days and this sorta fixes the problem since it lets you read/move/delete anything from the last month but if you need to check something older while mobile you may have to use the web client ..
hope this helps ..