I had a working @mac.com email address as of July 9, 2008 and moved to iCloud before August 1, 2012. My Apple ID and primary email address is my @mac.com address.
On September 28 all new messages sent to my aliases now appear in my primary email inbox rather than the alias inbox's. This condition is the same in all email clients including 3rd party Apps, not just Apple Mail Apps on my iMac and iOS devices and the iCloud web mail browser.
What happens if you delete the alias and recreate it with a test email?
Do you mean aliases which are additional addresses to the main one, or are you referring to the @mac.com and @me.com versions of the @icloud.com address (i.e. the same text before the '@') - strictly speaking these are not aliases? If the latter, you cannot delete any of them: if the former, be aware that when you delete an alias you can't restore it.
In any event, all incoming messages go to the inbox, whether addressed to versions of the main address or the aliases, unless Rules are used to direct them elsewhere. If you have extra mailboxes for different addresses you must have created them yourself and set up Rules to move incoming messages to specific addresses to the equivalent mailboxes, so possibly the Rules have been broken and you will have to set them up again.
Messages to aliases are going to main iCloud address
