In part, I think it's because there is still good work that goes on under the W3C umbrella in other areas; the CSS working group has managed to stay reasonable, learn from the mistakes of some over-engineered past standards, and continues to work with implementers.

Also, there are reasons to want some of what the W3C provides that the WHATWG doesn't. The W3C has many more member companies, and it can get them to sign off on patent rights so there's less likelihood of some one of Adobe's patents on page layout in InDesign suddenly being infringed by web browsers due to something in the spec.

And finally, I think that the W3C wants to stay relevant and so it keeps on trying to work from a basis on the WHATWG spec, and promising it will be good this time, and then it goes off and pulls this stuff again.