What Deadsea and diberry said, plus several other possibilities....
In the Matt Cutts video on Google's October 16th blogspot announcement, Matt made it very clear that they won't honor disavow requests in extreme cases where you might shoot yourself in the foot, and disavowing all links is extreme. He also made it very clear that Google wants the site owner to do most of the work. Probably there are several reasons for this.
One is that they'd like the links physically out of the index. It makes life easier for them, as it will scale better going forward.
But also, IMO, Google wants to get some useful information out of this. They want good leads to bad sites and networks, and 100% disavows could cloud the picture enough that the data isn't useful. Choosing everything is revealing nothing.
As you described above, in the first 70% you went after "mostly directories, blog-rolls and low quality sites." In other words, the obvious suspects. Your post isn't quite clear how hard you tried on the remaining 300.
I'd bet that Google wants leads on the not-so-obvious suspects, and might feel that you're withholding information, that your blanket disavow of the remaining 300 domains is a cop-out. This is just a guess, but I assume these reasons have something to do with why Google wants the site owners to do a bunch of the work.
I'm curious, btw, whether Google has a separate message for "we don't think you've tried hard enough before you used the tool", or whether what you received is the blanket "no" for everything.