This particular user had her options set to hide filed messages by setting in Messages | Options | Hide Filed Messages to "Yes". She then moved some messages to folders on her Blackberry. She did this by opening the message, then clicking "File" and picking the appropriate folder. She did this a bunch of times, then the Blackberry froze up. When it came back after she clicked the "Back" button and waited, a bunch of her messages were back in her Inbox on her Blackberry again. We ran "Delete Prior" on them and noticed the setting for "Hide Filed Messages" was set to "No".
We are on a BES Server using Lotus Notes 7.0.2. This has happened to her 3-5 times in the past and even on different Blackberry hardware.