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Not that I've noticed... I started with the company back in February and noticed it when I crawled the site with Screaming Frog. So they already had uppercase and lowercase permalinks back then. When I brought it to our developers attention they didn't seem to concerned. Then I saw something somewhere that discussed Google seeing them as potential duplicates. Which is when I posted to MOZ and got the response that it was fine since we have canonical URLs in place. So, it has not had any negative effect since I started that I can see. However, I don't know how to correct Screaming Frog from seeing as duplicate pages.

A site running ASP should be perfectly fine. I bet you will see substantial increases in a lot of positive metrics by just pairing down that navigation.