HE-AAC files should show up, I think. They just may not play at full speed.
fri, you didn't mention whether or not you're getting entries in the database that look like
< Untagged >
.
Also, if you check the versions that you have on your computer with a proper tagging tool can you verify that they are properly tagged? I have seen situations where iTunes will not write metadata tags to the file, but will store the info in its own database.