Can you put one of your scans somewhere, like www.dropbox.com, and post a public download/share link to it? I'd like to try one of the scans on my computer, though, to see if it does the same thing. You can crop an original down to something smaller that includes sky and trees like your screenshots show.
I am guessing there is a gamma problem or a profile problem somewhere. What Profile do the scans have embedded in them from the scanner? You can turn on the three Ask checkboxes in your color-settings and see what it says when you open an original in Photoshop.
My guess is that LR is using a default profile that doesn't match what Photoshop is using, but perhaps there is a gamma issue, too.
Have you tried opening one of the originals in the Camera Raw plug-in, perhaps from Bridge or just from PS / File / Open. You may have to set your PS Camera Raw settings to prefer ACR for TIFs. ACR and LR should be about the same in file handling so it'd be interesting to see if that is the case.