I'm currently activated on my companies BES server. My email reconciliation message service is set to Web Client, but when I send or or reply to emails it's using my companies email correspondence, any ideas why?

You can configure the reconciliation separately for each of the services. Just go back to Messages->Options->Email Reconciliation. Highlight "Web Client" and press on the space bar. It should change to "Desktop" and there you can configure your email reconciliation options for your BES account.