It appears that there was a cascade of problems on this.
One Friday evening, our file/mail/fax server locked up, and when I rebooted it the USB modems didn't come on line. Eventually I managed to unplug the serial adapter and restart the hotplug and usb drivers in the right order, and that started working, but a day or so later they told me they still weren't getting any faxes.
I went through a few daily checks to make sure I was getting "Running and idle" from faxstat, and it eventually cascaded that the faxes were being received just find, but were not beign delivered.
First error was that mysql had been removed in a clean-up attempt, because the MySQL daemon wasn't even running. It turns out that Cyrus (or was it postfix?) was depending on it, but there doesn't seem to be a reliable way to determine specific dependencies of an installed package in Gentoo right now.
Once that was working and Cyrus, Postfix, and Hylafax were all at least running, we still had problems. Logs said that delivery to /home/faxes/.maildir/tmp...etc. wasn't working.
Bill C. helped me find the "mailbox_transport = cyrus" option in main.cf, which had aparently been overwritten by an update which I didn't catch with etc-update.
Next cascading error was that /cyrus/bin/deliver wasn't found. For some reason, Gentoo was unable to determine where Gentoo had installed the cyrus binaries, and the postfix master.cf file needed to be updated with the actual path (/usr/lib/cyrus...).
Complicating this was that this morning, when I actually sat down to put the time in to work the problem all the way through instead of just doing trivial checks, our Business Class RoadRunner connection started intermittently dropping packets, then started bungee jumping up and down. 40% packet loss makes it pretty hard to do a coherent diagnostic, but I think it's working all the way through now.
The reason this was so complex to solve is that I kept doing little system diagnostics of the aparent immediate problem, like checking the modes with faxstat, but not doing an all-the-way-through trace to make sure that all the pieces were working. With the usb hub, cyrix, and postfix all having problems, it wasn't untill I walked a message all the way through the system that I solved it all.
Thanks for the help!