Okay so the problem is not from the BB to your mail client but the other way around.
How does your laptop connect to the network? When? How Long?
What mail program do you use? Outlook? Notes?
Which 4.1.x version is your BES?
Do the ones who are left of the "some quantity" have a mail icon or a folder icon?
Do you have folder redirection enabled for all folders? Maybe you created new ones?
Can you confirm that the messages have been moved om the mail server by looking into the web client (like for example through Outlook Web Access)