That's it! Was having the same issue ... I changed my Transparency blend space to RGB and that fixed the problem with my photos. RGB photos were coming out as faded when I exported to an RBG pdf. The only other solution was to flatten the pdf. But changing the transparency flattener colorspace to RBG fixed the problem so that I don't have to flatten the document first. Thanks!!!
I was having the same problem, I am not techy at all just getting started with IndesignC3. So I can't give much insight into the actual issue but i did fix washed-out problem I was having, so maybe this can work for you guys too.
When I was exporting to pdf under: settings-general, in the top right is 'compatibility'. At first it was set at Acrobat 5 (PDF 1.4). I changed it to Acrobat 4 (PDF 1.3) and it is woking...no washed out look!
Hope it can work for you guys too.