A WebmasterWorld thread has an interesting discussion around how a webmaster said his manual penalty was revoked on his WWW but remains on his non WWW.
The non WWW is 301 redirected to the WWW and the WWW is set as the preferred domain in Webmaster Tools.
The webmaster with this problem said:
A site I watch has a manual penalty. After a lot of link cleaning and reconsideration request, Google has revoked penalty on www version, while penalty on non-www version stays. Both www and non-www versions verified in WMT and 301 redirected from non-www to www.Its about a week now since penalty on www was revoked and the site doesn't even rank for domain.com.
Have you ever seen this case, where the WWW vs the non WWW don't have timed penalties properly?
Forum discussion at WebmasterWorld.
Image credit to BigStockPhoto for traffic cones
