Hi!
flashrom v0.9.3-r1205 on FreeBSD 8.1-RELEASE (i386), built with libpci 3.1.7, GCC 4.2.1 20070719 [FreeBSD], little endian flashrom is free software, get the source code at http://www.flashrom.org
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we have split that chip definition into two parts some time ago (the W39V040C version has an LPC interface, the W39V040FC is FWH-compatible; probably write protection also differs and that's the reason for said change, but i am not entirely sure).
afaics your board/chipset configuration supports both buses, hence your report does not really help. a retest with the latest stable version (0.9.4) or a development snapshot would be appreciated! it would probably detect both chips and you would have to select the correct one.
I've made a patch to update flashrom in the fbsd ports to 0.9.4 and will report back.
http://www.freebsd.org/cgi/query-pr.cgi?pr=159708