Welcome to Crackberry.
With your first problem, I believe your problem is due to the age of your messages in the folders. When you first sync, BES(x) will only sync messages not older than 10 days to your phone (by default). If you added Folders to sync after this initial sync, then you will only see the messages you place in these folders from that point forward, the old messages will remain within your e-mail system (outlook/notes??), but your BB will not have access to them.
As far as your second problem, is this on all messages you try to send or just ones going to other people within your company's e-mail system (outlook/notes)?