I just got out of the ad agency after working full time for several years while freelancing in my spare time. Agency experience is perceived negatively in the startup community because it's common knowledge that most agencies don't treat developers well. Mediocre developers often get high rates because there's such a lack of developers willing to put up with the kind of work (stressful, low budget, extremely short deadlines, not much room for polishing). A developer coming from an ad agency with "Javascript" on their resume is likely to only know enough jQuery to get by.

That said, it's often possible to differentiate yourself from the crowd by using phrasing that only knowledgeable developers use or listing a more detailed toolset that shows the same (eg: "Javascript, jQuery" vs "OO Javascript, jQuery, Backbone.js").