In outlook I have a lot of rules setup to move emails to personal folders. My blackberry will see the emails for a couple of minutes until it reconsiles itself and then the emails will disappear. Anything that shows up in the inbox though stays.

Any suggestions to to keep the emails from disappearing in the blackberry?

The way you have it set up ... no, there isn't.
If you were filing to folders within your Outlook mailbox on the Exchange server, then you could. However since you're filing to Personal Folders, the BlackBerry device will "lose track" of the messages and basically treat them as being deleted.

Figured as much. Just wanted to ask and make sure.

Thanks.