in /etc/conf.modules netcfg put "ne io=0x300" and "ne io=0x240" .... The second one replaces the first so the first ethernet card is not found. netcfg should use "ne io=0x300,0x240".
netcfg never writes to /etc/conf.modules. Perhaps you were using linuxconf?
I think that "netcfg" was a typo for "netconf" which is part of linuxconf. I've since heard of this bug in linuxconf from other folks.
This should be fixed in linuxconf-1.16r10-1 (or later) that we will release as an errata update after testing.
1.16r10-2 released