The Bes server scans the inbox for new e-mails.
If you have a rule on the inbox that moves mails out of the inbox then the mails will never appear on your blackberry as they never appear in your inbox.
Changing hide filed messages will not help either (set Hide filed messages back to yes)..
If you do not have access to your bes server then you can do the following from your blackberry device.
Select the button to the left of your scroll wheel. (so do not click the scroll wheel).
Select Folder “Folder Redirection”
Expand your mailbox
and put a tick on all the folders where you have rules moving them from out of your inbox.
So that you can see messages that are subfolders to your to your Outlook Inbox, make sure on the BlackBerry that you go into messages > Options > Email Settings > Press for Menu and choose Folder Redirection. Expand the plus next to Mailbox – Name. Go down to Inbox and expand plus next to Inbox (menu > select Expand. Now, make sure that any subfolder that you want the messages to appear on the BlackBerry are checked. Then save the settings. Messages that are automatically redirected to subfolders that are not .pst files will appear on the BlackBerry.