Hi James,
Google's Disavow Tool is not a first line of defence, but the last.
Matt Cutts made it quite clear when releasing the tool that Google still expects webmasters to make a "good faith effort" to remove as many links as possible before using the Disavow Tool.
If you read Dr Pete's post using the link that Smart Lock Solutions provided in their post you can see this. If you have not seen the video from Matt Cutts about the Disavow Tool, you can watch it and read some views on the release of the tool here.
The only way to confirm whether a manual penalty has been applied is to lodge a reconsideration request. The webspam team will respond to a request, either advising that there is no manual action in place, or that a penalty exists because the site violates their search quality guidelines.
Hope that helps,
Sha

