Emails from our own domain are going into the Spam folder in Outlook

Hi there,

Our outlook has two (what seems like) server generated folders: Junk email and Spam Mail.

We recently updated our security certificate and ever since then, we have had emails that are not spam go straight to users' spam folder.  These emails would only show in the Spam email folder and would be absent from the junk email folder.  This happens with external email senders as well as internally with our own domain email addresses.  I was under the impression that, by default, outlook 2010 or exchange server 2010 wouldn't send emails from within our own domain to either the junk or spam folder and when we still had our old security certificate loaded (which is now expired) we never had our own domain users' emails going to the spam folder.

I first tried right clicking on the email (from one of our own domain users), went to junk email options, chose never block sender as well as never block sender's domain yet the email continues to show up in the Spam folder.

I've already checked three different websites to see if our IP address or domain is blacklisted but all of the scans come back saying that neither our IP or mail server is blocked.

For troubleshooting purposes, I also went on my outlook client and turned off automatic junk email filtering

I then went on our exchange 2010 server, launched exchange mangement shell and ran the command:

Set-MailboxJunkEmailConfiguration -Identity User1 -Enabled $false

and turned off junk email for myself from the server.

I also ran the command:

Set-OrganizationConfig -scljunkthreshold 9

And played with setting the value to 0, 5, and 9 which again didn't seem to affect the Spam folder on my outlook client.

After each troubleshooting task above, I closed my outlook client and restarted it but all those troubleshooting steps yielded to no result as i continued to see emails from our domain users go into the Spam folder.  Again, I want to make it clear, these emails are not going in the Junk email folder on my outlook client but they bypass the inbox and go straight to the Spam email folder in outlook.

Do I need to restart our exchange server services on our server after running those power shell commands?  Is there any other way to turn stop email going straight to the Spam folder?

Thanks.