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Have you checked the SMTP logs? You might be hitting the recipient rate limits or ending up in the high-risk pool.
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Have you checked the SMTP logs? You might be hitting the recipient rate limits or ending up in the high-risk pool.

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I have an SMTP server (Server 2012 R2 using IIS6) that points to our Smart host at Microsoft for O365. This is the only SMTP server on premise. We have users with our normal domain (@company1.com) but also some users that have aliases setup as (@company2.com). The aliases are setup correctly in O365 portal as you can send email to them from outside the network. But when our scanners (which are what we use the SMTP server for) try to scan to them, the @company1.com gets delivered right away, but the @company2.com seems to get stuck in the inetpub\mailroot\Queue folder. They do deliver eventually but it can be anywhere from 30 minutes to 3 hours later. Microsoft said it's not there ned and that the delay is leaving our SMTP server. Any ideas? I did add a Remote Domain of company2.com as well to see if that works, but still no luck.
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I have an SMTP server (Server 2012 R2 using IIS6) that points to our Smart host at Microsoft for O365. This is the only SMTP server on premise. We have users with our normal domain (@company1.com) but also some users that have aliases setup as (@company2.com). The aliases are setup correctly in O365 portal as you can send email to them from outside the network. But when our scanners (which are what we use the SMTP server for) try to scan to them, the @company1.com gets delivered right away, but the @company2.com seems to get stuck in the inetpub\mailroot\Queue folder. They do deliver eventually but it can be anywhere from 30 minutes to 3 hours later. Microsoft said it's not there ned and that the delay is leaving our SMTP server. Any ideas? I did add a Remote Domain of company2.com as well to see if that works, but still no luck.

Email stuck in queue, IIS 6, Server 2012 R2

Interactions between email servers and clients are governed by email protocols. The three most common email protocols are POP, IMAP and MAPI. Most email software operates under one of these (and many products support more than one).  The correct protocol must be selected, and correctly configured, if you want your email account to work.

Email Protocols

Windows Server 2012 is the server version of Windows 8 and the successor to Windows Server 2008 R2. Windows Server 2012 is the first version of Windows Server to have no support for Itanium-based computers since Windows NT 4.0. Windows Server 2012, now in its second release (Windows Server 2012 Release 2) includes Foundation, Essentials, Standard and Datacenter, and does not support IA-32 or IA-64 processors.

Windows Server 2012

Office 365 is a group of software plus services subscriptions that provides productivity software and related services to its subscribers. Office 365 allows the use of Microsoft Office apps on Windows and OS X, provides storage space on Microsoft's cloud storage service OneDrive, and grants 60 Skype minutes per month. Office 365 includes e-mail and social networking services through hosted versions of Exchange Server, Skype for Business Server, SharePoint and Office Online, integration with Yammer, as well as access to the Office software. All of Office 365's components can be managed and configured through an online portal; users can be added manually, imported from a CSV file, or Office 365 can be set up for single sign-on with a local Active Directory using Active Directory Federation Services.