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.
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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A change I made fixed it.