I recently did an upgrade to SharePoint 2013 in my organization and everything went pretty much according to plan except for the incoming e-mail part of the farm decided to stop working. I set all my exchange routes to route mail to the new server and mail was routing, but it would just sit in the drop box and SharePoint would never pick it up.
So on to troubleshooting. I tried putting the smtp server on two of my front end servers and make sure the services were running. They were, mail sitting in drop folder, but it never would pick them up. I tried making sure permissions were right on the folders and they were. Tried everything according to documents of setting up the incoming e-mail. I've never had issues before with this. Moved it to the app server and still nothing. I researched and could not find anything, even combed through logs couldn't find any errors. I'm not the best ULS log viewer, but I figured it would at least spit an error or something but I couldn't find anything, maybe I need to turn my logging level up or something.
What was the fix you might ask? It all ended up being what I thought it might of been from the beginning was file permissions, but setting permissions on the folder would not work, even giving full admin rights to the service account wouldn't pick up the file. It wasn't until I setup a File Share to the drop location and configured the incoming e-mail settings to pickup the drop e-mail from the file share Location.
Once I did this, low and behold the e-mail started processing. I don't really have the time to go in and figure out exactly what is wrong, but my gut tells me that something with Windows 2012 is preventing that service from directly accessing anything in that folder directly.
Anyway, hopefully this may help some of you guys out when it comes to trying to figure out incoming e-mail problems with SharePoint 2013 and Server 2012. Also don't forget the incoming e-mail quota bug ( I say it's a bug, Microsoft did it by design apparently now), where you must have a quota set for it to work as well, here is the link to that: http://social.technet.microsoft.com/Forums/sharepoint/en-US/a82e1a6f-4184-4815-9f46-4009a5341bfd/incoming-email-stuck-in-drop-folder-after-sphotfix-installation
Let me know if this fixes this issue for your upgrade, would like to know. Thanks!