With Lightroom 2 and 3, I experience a modest loss of saturation when exporting, or when editing in Photoshop. I have LR edit in Photoshop set to create a 16 bit Prophoto Tiff. When I export from Lightroom, I can export as an sRGB jpeg or a 16 bit Prophoto Tiff, and the result is the same. When I do an edit in Photoshop, the saturation loss is immediately evident in Photoshop, as well as in the Lightroom preview that is generated as soon as the image opens in Photoshop. It doesn't seem to matter if the file I am exporting from is a RAW, Tiff or PSD. However, it seems that, if I do an edit in Photoshop, and add back some saturation and vibrance (roughly +20 vibrance and +8 saturation) there, when I save the image back to Lightroom, I can then export it without the saturation loss. I am viewing in color managed applications, and I calibrate my monitor (Eye1 Display 2).
Has anyone else seen this? By the way, I have had no issues with printing from Lightroom.