I just had a very similar problem on a 486/dx66 with Phoenix BIOS.  The
3c509 (ep0) worked fine after I removed the `ie' driver (I was always
getting `ie0: unknown AT&T board type xx' at probe time).  Prior to that,
the probe missed the 3c509 upon warm start.  If you haven't done so
already, I'd try removing `ie' driver lines from your kernel config.

Dave Deaven <deaven@ishmael.ameslab.gov>

>
>>Number:         753
>>Category:       port-i386
>>Synopsis:       Kernel doesn't recognizes 3c509 Ether Card after warm reset.
[...]

>>Description:
>When rebooting, the kernel doesn't seem to recognize ep0 (Etherlink III).
>We have 3com original cards. We have tested a couple of them, and seem 
>to work the same way... If you boot right after switching on, the
>card is recognized and works after ifconfig link0 link1. Iportant:
>The problem only manifests itself after rebooting (warm reset).
>>How-To-Repeat:
>Plug in a Etherlink III, boot the machine with NetBSD, reboot after
>booting is complete, without switching off the machine. It can be
>seen that ep0 doesn't appear in the screen...
>>Fix:
>Currently, only don't warm reboot ;-)