original my destination look like
mydestination = $myorigin,$myhostname,localhost,localhost.$mydomain,$mydomain
after change (for domain acme.com)
mydestination = $myorigin,$myhostname,localhost,localhost.$mydomain,$mydomain,acme.com
Going off of what branislav.kopun wrote I started poking around in the stubs. His workaround still works (just added a comma and typed in the name of my virtual domain on the end), but I wanted to figure out what variable was missing.
Haven't found anything yet, several spots refer to objectClass=CourierVirtualDomain (and CourierMailAlias etc...) when Dovecot is installed instead of Courier, but changing that didn't seem to have any effect.
I tried guessing at the variable name (assuming that was what was missing) and it's not $vdomain, $vdomains, $vdomainsCfFile, or $virtual_mailbox_domains (all of which were things I came across in the files and decided to try). I thought that last one would work, because it looked to be formatted the same way as some of the other declarations in the main.cf.mas
Speaking of formatting, I compared the vdomains.cf.mas and the valiases.cf.mas files and found the "query_filter = " line backwards in vdomains compared to valiases and tried flipping it around, but no dice.
SHORT VERSION:
branislav.kopun's workaround of manually putting in the virtual domain still works.
I tried a bunch of stuff to find the problem (missing parameter?) that didn't solve it.