So Google’s Penguin 3.0 roll out came and went (well, we are not 100% confident it is done rolling out). In any event, not everyone who was hit by previous Penguin penalties notices a recovery.

Google’s John Mueller responded to one such webmaster who as in that exact situation.

The webmaster posted in the Google Webmaster Help forums and John responded as follows:

So let me pull out the highlights from here, if any:

When you submitted your disavow file matters
How quickly Google processed the file, the links and when the algorithm ran is important
You may have missed critical and harmful links when disavowing

This is one of those very generic responses from Google that is not always that helpful but gives you some background on how these algorithms work a bit.

Forum discussion at Google Webmaster Help.