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I added media.module to my site and set it up to add a field to the Article content type. When I click the 'select media' link, the pop up window is 2 px high - it looks like it starts to render at the correct size (height 550 I think) but ultimately it is 2 px high.
if I change height to 500 or so, I can see the whole window. I tried in bartik in chrome and ff and the window seems to work.