If the exchange server is identifying the email as junk then you may need to adjust the antispam setting on the server, because all users don't have this issue it may not be the problem.
I would start by whitelisting the email addresses the printers/scanners are using to send the email. Whitlist in exchange antispam filters, whitelist in outlook junkmail senders.
Outlook has two different mode online and offline, in online mode spam will not filter anything, the spam rules actually don't do anything, in offline mode they do, it may be that you have some outlooks in online mode and some in offline mode. in outlook look to see that exchange caching is turned on, if it is then you are in offline mode. The same behavior happen when you don't have outlook open, junk comes in and goes to inbox because outlook junk filter is not running, user opens outlook message then gets filtered and goes to junk mail.
in exchange 2010 with antispam filters
Set-ContentFilterConfig -BypassedSenderDomains Microsoft.com
here is a quick link I found that explains how to whitlist more than one domain
http://dan-israel.com/blog/it/exchange-2010-whitelist/
Hi Jason,
Outlook emails ending up in Junk folder could be caused due to several reasons.
We can use the following registry key to totally disable Outlook Junk email filter to determine if this issue is caused by the Outlook Junk Filter feature:
HKEY_CURRENT_USER\Software\Policies\Microsoft\office\15.0\outlook
DWORD: DisableAntiSpam
Value of 1 disables the junk filter, 0 enables it
If this issue still persists, it means the emails are not filtered by Outlook. We can change the key value to 0 and check if the users have any virus scanner installed. We may try disabling the scanner integration in Outlook according to the documentation of the software, and then test the issue again.
Please let me know the result.
Regards,
Steve Fan
TechNet Community Support