Have you isolated when / where your long tail phrases Yo Yo or show differently on different data sets ? - i mean if you are not getting traffic it must mean that at times your results are not showing
Yes - that is the thing to discover. That and why it isn't happening in a more widespread fashion.
In the two cases I've been able to investigate (one a major enterprise site and one more entrepreneurial) both showed a lack of diversity in their backlinks. That is, it didn't look like either had many truly free editorial links, where someone just naturally decided to link to them. Neither seemed to have obvious guideline infractions either, but their backlink profiles were kind of lopsided.
That is only an observation, not a conclusion. There's no way two cases justifies a conclusion.