I saw many of websites that submitted to my directory and the only backlink noticed by Google comes from it. This is just as I check my stats from time to time and as a referer I see Google with query: 'link:www.domain.com" See even for those sites submitted in JUNE as Google made some update in backlinks recently. Also among my own baacklinks I see many from other directories. Remember it always takes some time until Google update new backlinks.
If the page your link appears on is indexed it gets counted irrespective of the "quality" of the directory or whether its in the suplementary index or not. Google quite simply takes a dim view of wide boys abusing the tools it provides.