Your app update goes into a different review queue, and people who are not be familiar with previous versions of your app will review it. They will pick on things that previous reviewers had already come to terms with (either through discussion with you, or lengthy review).
Edit: more info, this happened with our app "Codea". Because it was a coding app for iPad, the initial review was extremely lengthy (over a month). When we had to urgently update due to a trademark issue, our "expedited" review also took over a month — as if it was being reviewed for the first time (despite having past updates reviewed quickly). It didn't seem to matter that the existing version was available all the while on the App Store, either.
Apple's review process is incredibly weird.