Zogby is probably still using the old Dem 39% Rep 36% IND 25% formula that pollers have used for years. He hasn't adjusted for the fact that it is now a 39%-39% electorate.
In 2000 Rasmussen adjusted, but he adjusted too far (in addition to using a flawed autmatic polling method) -- I think his numbers were actualy in the 38%-36% range for Republicans.
Automated telephone polling in and of itself doesn't make the methodology flawed. SurveyUSA uses automated telephone polling and they've been one of the more reliable polling organizations of late. From what I understand, Rasmussen has conceded he used too tight a screening method in 2000. He has loosened it this year.