We are running exchange 2016 and having issues with transport rules. We had the same issues on exchange 2010. We have a basic rule that looks for messages going to customer service, and it forwards those messages to our ticket queue. This used to work fine, but now has just stopped working. I've been googling for some time now, with no answers. Some things we have been looking at:
Set-TransportConfig -ShadowRedundancyEnabled $false (didn't fix it)
Get-MessageTrackingLog (not sure this is helping)
Would appreciate any direction you can give.