This question comes up constantly.
First, are you doing Mailbox backups, or Information store backups?
If mailbox backups, not only are you not protecting your data, but that would totally account for your performance. Mailbox backups work by opening a MAPI session and simply downloading every individual email- it was never meant to run very fast.
If an email contains a virus or similar and is blocked by your scanner, you will receive this error.
Again, simply using the Information Store style backup usually resolves this.