ZydoSEO - 4:00 am on Mar 1, 2013 (gmt 0)
Google has said repeatedly over the years that the output from the LINK: operator as well as the links listed in WMT are BOTH samples. WMT typically gives a larger sample than LINK:, but still it is just a sample.
While Google does want you to attempt to take down those links violating their guidelines before using the Disavow Tool, I doubt this is necessarily a requirement. I think they ask that you do so for selfish reasons... to save themselves from having to continue to process those links ad infinitum and to miminize the number of links disavowed (and the processing required to disavow them). Imagine the CPU cycles spent processing and disk space required to store all of the webspam links on the Internet.
If Google's response to your RR specifically said, "we still see links to your site that violate our quality guidelines" then that is likely the reason your RR was rejected.
I would try to determine "why" they were still seeing "bad" links. Perhaps you missed some that were not shown in the WMT sample of links... Or perhaps you submitted the RR too soon after disavowing your links.
Did you want 3-4 weeks after disavowing those links BEFORE submitting your Reconsideration Request? Google stated very clearly in their original post on their blog that it can take weeks to process your disavows (i.e. recrawl all those links and essentially flag them NOFOLLOW):
We need to recrawl and reindex the URLs you disavowed before your disavowals go into effect, which can take multiple weeks.
They also stated you should allow time for the disavows to process before submitting an RR:
Wait for some time to let the disavowed links make their way into our system. Finally, submit a reconsideration request so the manual webspam team can check whether your site is now within Google's quality guidelines, and if so, remove any manual actions from your site.
Submitting a RR before Google's had time to process all of the disavowed links "might" cause them to still show in their tools used to review your link profile as essentially "followed" links that are still flowing PR.
If you feel you allowed sufficient time for Google to process your disavows before submitting your RR, then I would recommend getting backlink data from as many sources as you can (Google WMT, Bing WMT, Majestic, OSE, etc.)... aggregate it... dedup it... and then review them all one-by-one. Remove and/or disavow any remaining links that appear suspect.